endoreg-db 0.8.5.1__py3-none-any.whl

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

Potentially problematic release.


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

Files changed (794) hide show
  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
  300. endoreg_db/mermaid/classification.md +8 -0
  301. endoreg_db/mermaid/examination.md +8 -0
  302. endoreg_db/mermaid/findings.md +7 -0
  303. endoreg_db/mermaid/image_classification.md +28 -0
  304. endoreg_db/mermaid/interventions.md +8 -0
  305. endoreg_db/mermaid/morphology.md +8 -0
  306. endoreg_db/mermaid/patient_creation.md +14 -0
  307. endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
  308. endoreg_db/migrations/0001_initial.py +1857 -0
  309. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  310. endoreg_db/migrations/0003_add_center_display_name.py +30 -0
  311. endoreg_db/migrations/__init__.py +0 -0
  312. endoreg_db/models/__init__.py +359 -0
  313. endoreg_db/models/administration/__init__.py +116 -0
  314. endoreg_db/models/administration/ai/__init__.py +9 -0
  315. endoreg_db/models/administration/ai/active_model.py +35 -0
  316. endoreg_db/models/administration/ai/ai_model.py +156 -0
  317. endoreg_db/models/administration/ai/model_type.py +41 -0
  318. endoreg_db/models/administration/case/__init__.py +19 -0
  319. endoreg_db/models/administration/case/case.py +114 -0
  320. endoreg_db/models/administration/case/case_template/__init__.py +15 -0
  321. endoreg_db/models/administration/case/case_template/case_template.py +125 -0
  322. endoreg_db/models/administration/case/case_template/case_template_rule.py +269 -0
  323. endoreg_db/models/administration/case/case_template/case_template_rule_value.py +86 -0
  324. endoreg_db/models/administration/case/case_template/case_template_type.py +26 -0
  325. endoreg_db/models/administration/center/__init__.py +13 -0
  326. endoreg_db/models/administration/center/center.py +67 -0
  327. endoreg_db/models/administration/center/center_product.py +64 -0
  328. endoreg_db/models/administration/center/center_resource.py +49 -0
  329. endoreg_db/models/administration/center/center_shift.py +88 -0
  330. endoreg_db/models/administration/center/center_waste.py +30 -0
  331. endoreg_db/models/administration/permissions/__init__.py +44 -0
  332. endoreg_db/models/administration/person/__init__.py +24 -0
  333. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  334. endoreg_db/models/administration/person/employee/employee.py +35 -0
  335. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  336. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  337. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  338. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  339. endoreg_db/models/administration/person/names/__init__.py +0 -0
  340. endoreg_db/models/administration/person/names/first_name.py +18 -0
  341. endoreg_db/models/administration/person/names/last_name.py +19 -0
  342. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  343. endoreg_db/models/administration/person/patient/patient.py +460 -0
  344. endoreg_db/models/administration/person/person.py +31 -0
  345. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  346. endoreg_db/models/administration/person/user/__init__.py +5 -0
  347. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  348. endoreg_db/models/administration/product/__init__.py +14 -0
  349. endoreg_db/models/administration/product/product.py +97 -0
  350. endoreg_db/models/administration/product/product_group.py +39 -0
  351. endoreg_db/models/administration/product/product_material.py +54 -0
  352. endoreg_db/models/administration/product/product_weight.py +47 -0
  353. endoreg_db/models/administration/product/reference_product.py +130 -0
  354. endoreg_db/models/administration/qualification/__init__.py +7 -0
  355. endoreg_db/models/administration/qualification/qualification.py +37 -0
  356. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  357. endoreg_db/models/administration/shift/__init__.py +9 -0
  358. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  359. endoreg_db/models/administration/shift/shift.py +51 -0
  360. endoreg_db/models/administration/shift/shift_type.py +108 -0
  361. endoreg_db/models/label/__init__.py +24 -0
  362. endoreg_db/models/label/annotation/__init__.py +12 -0
  363. endoreg_db/models/label/annotation/image_classification.py +84 -0
  364. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  365. endoreg_db/models/label/label.py +83 -0
  366. endoreg_db/models/label/label_set.py +53 -0
  367. endoreg_db/models/label/label_type.py +29 -0
  368. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  369. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  370. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  371. endoreg_db/models/label/video_segmentation_label.py +31 -0
  372. endoreg_db/models/label/video_segmentation_labelset.py +27 -0
  373. endoreg_db/models/media/__init__.py +16 -0
  374. endoreg_db/models/media/frame/__init__.py +3 -0
  375. endoreg_db/models/media/frame/frame.py +111 -0
  376. endoreg_db/models/media/pdf/__init__.py +11 -0
  377. endoreg_db/models/media/pdf/raw_pdf.py +613 -0
  378. endoreg_db/models/media/pdf/report_file.py +162 -0
  379. endoreg_db/models/media/pdf/report_reader/__init__.py +7 -0
  380. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  381. endoreg_db/models/media/pdf/report_reader/report_reader_flag.py +20 -0
  382. endoreg_db/models/media/video/__init__.py +8 -0
  383. endoreg_db/models/media/video/create_from_file.py +358 -0
  384. endoreg_db/models/media/video/pipe_1.py +213 -0
  385. endoreg_db/models/media/video/pipe_2.py +105 -0
  386. endoreg_db/models/media/video/refactor_plan.md +0 -0
  387. endoreg_db/models/media/video/video_file.py +699 -0
  388. endoreg_db/models/media/video/video_file_ai.py +443 -0
  389. endoreg_db/models/media/video/video_file_anonymize.py +349 -0
  390. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  391. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  392. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  393. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  394. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  395. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  396. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  397. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  398. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  399. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  400. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  401. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  402. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +141 -0
  403. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  404. endoreg_db/models/media/video/video_file_frames.py +0 -0
  405. endoreg_db/models/media/video/video_file_io.py +168 -0
  406. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  407. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  408. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  409. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  410. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  411. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  412. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  413. endoreg_db/models/media/video/video_file_segments.py +209 -0
  414. endoreg_db/models/media/video/video_metadata.py +65 -0
  415. endoreg_db/models/media/video/video_processing.py +152 -0
  416. endoreg_db/models/medical/__init__.py +146 -0
  417. endoreg_db/models/medical/contraindication/__init__.py +17 -0
  418. endoreg_db/models/medical/disease.py +156 -0
  419. endoreg_db/models/medical/event.py +137 -0
  420. endoreg_db/models/medical/examination/__init__.py +9 -0
  421. endoreg_db/models/medical/examination/examination.py +148 -0
  422. endoreg_db/models/medical/examination/examination_indication.py +278 -0
  423. endoreg_db/models/medical/examination/examination_time.py +49 -0
  424. endoreg_db/models/medical/examination/examination_time_type.py +41 -0
  425. endoreg_db/models/medical/examination/examination_type.py +48 -0
  426. endoreg_db/models/medical/finding/__init__.py +18 -0
  427. endoreg_db/models/medical/finding/finding.py +96 -0
  428. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  429. endoreg_db/models/medical/finding/finding_intervention.py +52 -0
  430. endoreg_db/models/medical/finding/finding_type.py +35 -0
  431. endoreg_db/models/medical/hardware/__init__.py +8 -0
  432. endoreg_db/models/medical/hardware/endoscope.py +65 -0
  433. endoreg_db/models/medical/hardware/endoscopy_processor.py +182 -0
  434. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  435. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  436. endoreg_db/models/medical/medication/__init__.py +19 -0
  437. endoreg_db/models/medical/medication/medication.py +31 -0
  438. endoreg_db/models/medical/medication/medication_indication.py +50 -0
  439. endoreg_db/models/medical/medication/medication_indication_type.py +39 -0
  440. endoreg_db/models/medical/medication/medication_intake_time.py +44 -0
  441. endoreg_db/models/medical/medication/medication_schedule.py +45 -0
  442. endoreg_db/models/medical/organ/__init__.py +35 -0
  443. endoreg_db/models/medical/patient/__init__.py +56 -0
  444. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  445. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  446. endoreg_db/models/medical/patient/patient_event.py +75 -0
  447. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  448. endoreg_db/models/medical/patient/patient_examination_indication.py +44 -0
  449. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  450. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  451. endoreg_db/models/medical/patient/patient_finding_intervention.py +40 -0
  452. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  453. endoreg_db/models/medical/patient/patient_lab_value.py +222 -0
  454. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  455. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  456. endoreg_db/models/medical/risk/__init__.py +7 -0
  457. endoreg_db/models/medical/risk/risk.py +72 -0
  458. endoreg_db/models/medical/risk/risk_type.py +51 -0
  459. endoreg_db/models/metadata/__init__.py +19 -0
  460. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  461. endoreg_db/models/metadata/model_meta.py +206 -0
  462. endoreg_db/models/metadata/model_meta_logic.py +343 -0
  463. endoreg_db/models/metadata/pdf_meta.py +89 -0
  464. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  465. endoreg_db/models/metadata/sensitive_meta_logic.py +730 -0
  466. endoreg_db/models/metadata/video_meta.py +332 -0
  467. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  468. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  469. endoreg_db/models/other/__init__.py +40 -0
  470. endoreg_db/models/other/distribution/__init__.py +44 -0
  471. endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
  472. endoreg_db/models/other/distribution/date_value_distribution.py +89 -0
  473. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
  474. endoreg_db/models/other/distribution/numeric_value_distribution.py +125 -0
  475. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
  476. endoreg_db/models/other/emission/__init__.py +5 -0
  477. endoreg_db/models/other/emission/emission_factor.py +94 -0
  478. endoreg_db/models/other/gender.py +27 -0
  479. endoreg_db/models/other/information_source.py +159 -0
  480. endoreg_db/models/other/material.py +28 -0
  481. endoreg_db/models/other/resource.py +22 -0
  482. endoreg_db/models/other/tag.py +27 -0
  483. endoreg_db/models/other/transport_route.py +33 -0
  484. endoreg_db/models/other/unit.py +32 -0
  485. endoreg_db/models/other/waste.py +27 -0
  486. endoreg_db/models/requirement/__init__.py +11 -0
  487. endoreg_db/models/requirement/requirement.py +767 -0
  488. endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
  489. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  490. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  491. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +95 -0
  492. endoreg_db/models/requirement/requirement_operator.py +176 -0
  493. endoreg_db/models/requirement/requirement_set.py +287 -0
  494. endoreg_db/models/rule/__init__.py +13 -0
  495. endoreg_db/models/rule/rule.py +27 -0
  496. endoreg_db/models/rule/rule_applicator.py +224 -0
  497. endoreg_db/models/rule/rule_attribute_dtype.py +17 -0
  498. endoreg_db/models/rule/rule_type.py +20 -0
  499. endoreg_db/models/rule/ruleset.py +17 -0
  500. endoreg_db/models/state/__init__.py +12 -0
  501. endoreg_db/models/state/abstract.py +11 -0
  502. endoreg_db/models/state/audit_ledger.py +150 -0
  503. endoreg_db/models/state/label_video_segment.py +22 -0
  504. endoreg_db/models/state/raw_pdf.py +187 -0
  505. endoreg_db/models/state/sensitive_meta.py +46 -0
  506. endoreg_db/models/state/video.py +232 -0
  507. endoreg_db/models/upload_job.py +99 -0
  508. endoreg_db/models/utils.py +135 -0
  509. endoreg_db/queries/__init__.py +5 -0
  510. endoreg_db/queries/annotations/__init__.py +3 -0
  511. endoreg_db/queries/annotations/legacy.py +158 -0
  512. endoreg_db/queries/sanity/__init_.py +0 -0
  513. endoreg_db/renames.yml +8 -0
  514. endoreg_db/root_urls.py +9 -0
  515. endoreg_db/schemas/__init__.py +0 -0
  516. endoreg_db/schemas/examination_evaluation.py +27 -0
  517. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  518. endoreg_db/serializers/__init__.py +147 -0
  519. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +223 -0
  520. endoreg_db/serializers/_old/raw_video_meta_validation.py +179 -0
  521. endoreg_db/serializers/_old/video.py +71 -0
  522. endoreg_db/serializers/administration/__init__.py +14 -0
  523. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  524. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  525. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  526. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  527. endoreg_db/serializers/administration/center.py +9 -0
  528. endoreg_db/serializers/administration/gender.py +9 -0
  529. endoreg_db/serializers/anonymization.py +69 -0
  530. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  531. endoreg_db/serializers/examination/__init__.py +10 -0
  532. endoreg_db/serializers/examination/base.py +46 -0
  533. endoreg_db/serializers/examination/dropdown.py +21 -0
  534. endoreg_db/serializers/examination_serializer.py +12 -0
  535. endoreg_db/serializers/finding/__init__.py +5 -0
  536. endoreg_db/serializers/finding/finding.py +54 -0
  537. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  538. endoreg_db/serializers/finding_classification/choice.py +19 -0
  539. endoreg_db/serializers/finding_classification/classification.py +13 -0
  540. endoreg_db/serializers/label/__init__.py +7 -0
  541. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  542. endoreg_db/serializers/label/label.py +15 -0
  543. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  544. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  545. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  546. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  547. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  548. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  549. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  550. endoreg_db/serializers/meta/__init__.py +19 -0
  551. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  552. endoreg_db/serializers/meta/report_meta.py +53 -0
  553. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  554. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  555. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  556. endoreg_db/serializers/meta/video_meta.py +39 -0
  557. endoreg_db/serializers/misc/__init__.py +14 -0
  558. endoreg_db/serializers/misc/file_overview.py +152 -0
  559. endoreg_db/serializers/misc/stats.py +33 -0
  560. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  561. endoreg_db/serializers/misc/upload_job.py +71 -0
  562. endoreg_db/serializers/misc/vop_patient_data.py +120 -0
  563. endoreg_db/serializers/patient/__init__.py +11 -0
  564. endoreg_db/serializers/patient/patient.py +86 -0
  565. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  566. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  567. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  568. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  569. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  570. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  571. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  572. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  573. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  574. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  575. endoreg_db/serializers/pdf/__init__.py +5 -0
  576. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  577. endoreg_db/serializers/report/__init__.py +9 -0
  578. endoreg_db/serializers/report/mixins.py +45 -0
  579. endoreg_db/serializers/report/report.py +105 -0
  580. endoreg_db/serializers/report/report_list.py +22 -0
  581. endoreg_db/serializers/report/secure_file_url.py +26 -0
  582. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  583. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  584. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  585. endoreg_db/serializers/video/__init__.py +7 -0
  586. endoreg_db/serializers/video/segmentation.py +263 -0
  587. endoreg_db/serializers/video/video_file_brief.py +10 -0
  588. endoreg_db/serializers/video/video_file_detail.py +83 -0
  589. endoreg_db/serializers/video/video_file_list.py +67 -0
  590. endoreg_db/serializers/video/video_metadata.py +105 -0
  591. endoreg_db/serializers/video/video_processing_history.py +153 -0
  592. endoreg_db/services/__init__.py +5 -0
  593. endoreg_db/services/anonymization.py +223 -0
  594. endoreg_db/services/examination_evaluation.py +149 -0
  595. endoreg_db/services/finding_description_service.py +0 -0
  596. endoreg_db/services/lookup_service.py +241 -0
  597. endoreg_db/services/lookup_store.py +122 -0
  598. endoreg_db/services/pdf_import.py +1159 -0
  599. endoreg_db/services/polling_coordinator.py +288 -0
  600. endoreg_db/services/pseudonym_service.py +89 -0
  601. endoreg_db/services/requirements_object.py +147 -0
  602. endoreg_db/services/segment_sync.py +155 -0
  603. endoreg_db/services/storage_aware_video_processor.py +344 -0
  604. endoreg_db/services/video_import.py +1258 -0
  605. endoreg_db/tasks/upload_tasks.py +207 -0
  606. endoreg_db/tasks/video_ingest.py +157 -0
  607. endoreg_db/tasks/video_processing_tasks.py +327 -0
  608. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  609. endoreg_db/templates/admin/start_examination.html +12 -0
  610. endoreg_db/templates/timeline.html +176 -0
  611. endoreg_db/urls/__init__.py +70 -0
  612. endoreg_db/urls/anonymization.py +32 -0
  613. endoreg_db/urls/auth.py +16 -0
  614. endoreg_db/urls/classification.py +39 -0
  615. endoreg_db/urls/examination.py +54 -0
  616. endoreg_db/urls/files.py +6 -0
  617. endoreg_db/urls/label_video_segment_validate.py +33 -0
  618. endoreg_db/urls/label_video_segments.py +44 -0
  619. endoreg_db/urls/media.py +226 -0
  620. endoreg_db/urls/patient.py +19 -0
  621. endoreg_db/urls/report.py +48 -0
  622. endoreg_db/urls/requirements.py +13 -0
  623. endoreg_db/urls/sensitive_meta.py +0 -0
  624. endoreg_db/urls/stats.py +46 -0
  625. endoreg_db/urls/upload.py +20 -0
  626. endoreg_db/urls/video.py +61 -0
  627. endoreg_db/urls.py +9 -0
  628. endoreg_db/utils/__init__.py +88 -0
  629. endoreg_db/utils/ai/__init__.py +9 -0
  630. endoreg_db/utils/ai/get.py +5 -0
  631. endoreg_db/utils/ai/inference_dataset.py +52 -0
  632. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  633. endoreg_db/utils/ai/postprocess.py +63 -0
  634. endoreg_db/utils/ai/predict.py +291 -0
  635. endoreg_db/utils/ai/preprocess.py +68 -0
  636. endoreg_db/utils/calc_duration_seconds.py +24 -0
  637. endoreg_db/utils/case_generator/__init__.py +0 -0
  638. endoreg_db/utils/case_generator/case_generator.py +159 -0
  639. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  640. endoreg_db/utils/case_generator/utils.py +30 -0
  641. endoreg_db/utils/check_video_files.py +148 -0
  642. endoreg_db/utils/cropping.py +29 -0
  643. endoreg_db/utils/dataloader.py +175 -0
  644. endoreg_db/utils/dates.py +60 -0
  645. endoreg_db/utils/env.py +33 -0
  646. endoreg_db/utils/extract_specific_frames.py +72 -0
  647. endoreg_db/utils/file_operations.py +58 -0
  648. endoreg_db/utils/fix_video_path_direct.py +141 -0
  649. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  650. endoreg_db/utils/hashs.py +153 -0
  651. endoreg_db/utils/links/__init__.py +0 -0
  652. endoreg_db/utils/links/requirement_link.py +193 -0
  653. endoreg_db/utils/mime_types.py +0 -0
  654. endoreg_db/utils/names.py +76 -0
  655. endoreg_db/utils/ocr.py +190 -0
  656. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  657. endoreg_db/utils/paths.py +95 -0
  658. endoreg_db/utils/permissions.py +143 -0
  659. endoreg_db/utils/pipelines/Readme.md +235 -0
  660. endoreg_db/utils/pipelines/__init__.py +0 -0
  661. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  662. endoreg_db/utils/product/__init__.py +0 -0
  663. endoreg_db/utils/product/sum_emissions.py +20 -0
  664. endoreg_db/utils/product/sum_weights.py +18 -0
  665. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  666. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  667. endoreg_db/utils/requirement_helpers.py +0 -0
  668. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  669. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  670. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  671. endoreg_db/utils/setup_config.py +177 -0
  672. endoreg_db/utils/translation.py +27 -0
  673. endoreg_db/utils/uuid.py +4 -0
  674. endoreg_db/utils/validate_endo_roi.py +19 -0
  675. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  676. endoreg_db/utils/validate_video_detailed.py +357 -0
  677. endoreg_db/utils/video/__init__.py +26 -0
  678. endoreg_db/utils/video/extract_frames.py +88 -0
  679. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  680. endoreg_db/utils/video/names.py +42 -0
  681. endoreg_db/utils/video/streaming_processor.py +312 -0
  682. endoreg_db/utils/video/video_splitter.py +94 -0
  683. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  684. endoreg_db/views/__init__.py +272 -0
  685. endoreg_db/views/anonymization/__init__.py +27 -0
  686. endoreg_db/views/anonymization/media_management.py +454 -0
  687. endoreg_db/views/anonymization/overview.py +216 -0
  688. endoreg_db/views/anonymization/validate.py +107 -0
  689. endoreg_db/views/auth/__init__.py +13 -0
  690. endoreg_db/views/auth/keycloak.py +113 -0
  691. endoreg_db/views/examination/__init__.py +33 -0
  692. endoreg_db/views/examination/examination.py +37 -0
  693. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  694. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  695. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  696. endoreg_db/views/examination/get_findings.py +41 -0
  697. endoreg_db/views/examination/get_instruments.py +18 -0
  698. endoreg_db/views/examination/get_interventions.py +14 -0
  699. endoreg_db/views/finding/__init__.py +9 -0
  700. endoreg_db/views/finding/finding.py +112 -0
  701. endoreg_db/views/finding/get_classifications.py +14 -0
  702. endoreg_db/views/finding/get_interventions.py +17 -0
  703. endoreg_db/views/finding_classification/__init__.py +13 -0
  704. endoreg_db/views/finding_classification/base.py +0 -0
  705. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  706. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  707. endoreg_db/views/label/__init__.py +5 -0
  708. endoreg_db/views/label/label.py +15 -0
  709. endoreg_db/views/label_video_segment/__init__.py +16 -0
  710. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  711. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  712. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  713. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  715. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  716. endoreg_db/views/label_video_segment/validate.py +226 -0
  717. endoreg_db/views/media/__init__.py +45 -0
  718. endoreg_db/views/media/pdf_media.py +386 -0
  719. endoreg_db/views/media/segments.py +71 -0
  720. endoreg_db/views/media/sensitive_metadata.py +314 -0
  721. endoreg_db/views/media/video_media.py +272 -0
  722. endoreg_db/views/media/video_segments.py +524 -0
  723. endoreg_db/views/meta/__init__.py +15 -0
  724. endoreg_db/views/meta/available_files_list.py +146 -0
  725. endoreg_db/views/meta/report_meta.py +53 -0
  726. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  727. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  728. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  729. endoreg_db/views/misc/__init__.py +63 -0
  730. endoreg_db/views/misc/center.py +13 -0
  731. endoreg_db/views/misc/csrf.py +7 -0
  732. endoreg_db/views/misc/gender.py +14 -0
  733. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  734. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  735. endoreg_db/views/misc/secure_url_validate.py +79 -0
  736. endoreg_db/views/misc/stats.py +220 -0
  737. endoreg_db/views/misc/translation.py +182 -0
  738. endoreg_db/views/misc/upload_views.py +240 -0
  739. endoreg_db/views/patient/__init__.py +5 -0
  740. endoreg_db/views/patient/patient.py +210 -0
  741. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  742. endoreg_db/views/patient_examination/__init__.py +11 -0
  743. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  744. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  745. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  746. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  747. endoreg_db/views/patient_examination/video.py +194 -0
  748. endoreg_db/views/patient_finding/__init__.py +7 -0
  749. endoreg_db/views/patient_finding/base.py +0 -0
  750. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  751. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  752. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  753. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  754. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  755. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  756. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  758. endoreg_db/views/pdf/__init__.py +11 -0
  759. endoreg_db/views/pdf/pdf_media.py +239 -0
  760. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  761. endoreg_db/views/pdf/reimport.py +161 -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 +483 -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 +61 -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 +329 -0
  785. endoreg_db/views/video/video_media.py +158 -0
  786. endoreg_db/views/video/video_meta.py +29 -0
  787. endoreg_db/views/video/video_processing_history.py +24 -0
  788. endoreg_db/views/video/video_remove_frames.py +48 -0
  789. endoreg_db/views/video/video_stream.py +306 -0
  790. endoreg_db/views.py +0 -0
  791. endoreg_db-0.8.5.1.dist-info/METADATA +383 -0
  792. endoreg_db-0.8.5.1.dist-info/RECORD +794 -0
  793. endoreg_db-0.8.5.1.dist-info/WHEEL +4 -0
  794. endoreg_db-0.8.5.1.dist-info/licenses/LICENSE +674 -0
@@ -0,0 +1,344 @@
1
+ from django.db import transaction
2
+ from pathlib import Path
3
+ import logging
4
+ import shutil
5
+ from datetime import datetime
6
+ from typing import Optional
7
+
8
+ from endoreg_db.models import VideoFile, AnonymizationTask
9
+ from endoreg_db.exceptions import InsufficientStorageError
10
+ # from endoreg_db.models.media.video.create_from_file import check_storage_capacity
11
+
12
+ logger = logging.getLogger(__name__)
13
+
14
+
15
+ class StorageAwareVideoProcessor:
16
+ """
17
+ Enhanced video processor with built-in storage management and automatic cleanup.
18
+ """
19
+
20
+ def __init__(self, auto_cleanup: bool = True, min_free_space_gb: float = 10.0):
21
+ self.auto_cleanup = auto_cleanup
22
+ self.min_free_space_gb = min_free_space_gb
23
+
24
+ def check_and_ensure_storage(self, required_space_estimate: int = None) -> bool:
25
+ """
26
+ Check storage capacity and perform cleanup if needed.
27
+
28
+ Args:
29
+ required_space_estimate: Estimated space needed in bytes
30
+
31
+ Returns:
32
+ True if enough space is available, False otherwise
33
+
34
+ Raises:
35
+ InsufficientStorageError: If space cannot be freed
36
+ """
37
+ try:
38
+ # Get current storage stats
39
+ total, used, free = shutil.disk_usage('/')
40
+ free_gb = free / (1024**3)
41
+ usage_percent = (used / total) * 100
42
+
43
+ logger.info(f"Storage check: {free_gb:.1f}GB free ({usage_percent:.1f}% used)")
44
+
45
+ # Check if we need emergency cleanup
46
+ needs_cleanup = (
47
+ usage_percent >= 95.0 or
48
+ free_gb < self.min_free_space_gb or
49
+ (required_space_estimate and free < required_space_estimate * 1.2)
50
+ )
51
+
52
+ if needs_cleanup and self.auto_cleanup:
53
+ logger.warning(f"Storage critically low ({usage_percent:.1f}%), performing automatic cleanup")
54
+ self._perform_emergency_cleanup()
55
+
56
+ # Re-check after cleanup
57
+ total, used, free = shutil.disk_usage('/')
58
+ free_gb = free / (1024**3)
59
+ usage_percent = (used / total) * 100
60
+
61
+ if usage_percent >= 98.0:
62
+ raise InsufficientStorageError(
63
+ f"Storage critically low even after cleanup: {usage_percent:.1f}% used, "
64
+ f"only {free_gb:.1f}GB free",
65
+ required_space=required_space_estimate or int(self.min_free_space_gb * 1024**3),
66
+ available_space=free
67
+ )
68
+
69
+ return True
70
+
71
+ except Exception as e:
72
+ logger.error(f"Storage check failed: {e}")
73
+ raise
74
+
75
+ def _perform_emergency_cleanup(self) -> int:
76
+ """
77
+ Perform emergency storage cleanup.
78
+
79
+ Returns:
80
+ Bytes freed
81
+ """
82
+ total_freed = 0
83
+
84
+ try:
85
+ # 1. Clean up extracted frames for completed videos
86
+ frames_freed = self._cleanup_completed_video_frames()
87
+ total_freed += frames_freed
88
+
89
+ # 2. Clean up upload cache older than 1 day
90
+ uploads_freed = self._cleanup_old_uploads(max_age_hours=24)
91
+ total_freed += uploads_freed
92
+
93
+ # 3. Clean up large log files
94
+ logs_freed = self._cleanup_large_logs()
95
+ total_freed += logs_freed
96
+
97
+ # 4. Clean up temporary files
98
+ temp_freed = self._cleanup_temp_files()
99
+ total_freed += temp_freed
100
+
101
+ logger.info(f"Emergency cleanup completed: {total_freed / (1024**3):.2f}GB freed")
102
+
103
+ except Exception as e:
104
+ logger.error(f"Emergency cleanup failed: {e}")
105
+
106
+ return total_freed
107
+
108
+ def _cleanup_completed_video_frames(self) -> int:
109
+ """Clean up frames for videos that have completed processing."""
110
+ total_freed = 0
111
+
112
+ try:
113
+ from django.conf import settings
114
+ frames_dir = Path(settings.BASE_DIR).parent / 'storage' / 'frames'
115
+
116
+ if not frames_dir.exists():
117
+ return 0
118
+
119
+ # Find videos with completed anonymization
120
+ completed_videos = VideoFile.objects.filter(
121
+ anonymization_tasks__status='done'
122
+ ).distinct()
123
+
124
+ for video in completed_videos:
125
+ # Find frame directories for this video
126
+ video_frame_dirs = list(frames_dir.glob(f"*{video.uuid}*"))
127
+
128
+ for frame_dir in video_frame_dirs:
129
+ if frame_dir.is_dir():
130
+ try:
131
+ # Calculate directory size
132
+ dir_size = sum(
133
+ f.stat().st_size for f in frame_dir.rglob('*') if f.is_file()
134
+ )
135
+
136
+ # Remove the directory
137
+ shutil.rmtree(frame_dir, ignore_errors=True)
138
+ total_freed += dir_size
139
+
140
+ logger.info(f"Cleaned frames for {video.uuid}: {dir_size / (1024**2):.1f}MB")
141
+
142
+ except Exception as e:
143
+ logger.warning(f"Failed to clean frames for {video.uuid}: {e}")
144
+
145
+ except Exception as e:
146
+ logger.error(f"Frame cleanup failed: {e}")
147
+
148
+ return total_freed
149
+
150
+ def _cleanup_old_uploads(self, max_age_hours: int = 24) -> int:
151
+ """Clean up old upload cache files."""
152
+ total_freed = 0
153
+
154
+ try:
155
+ from django.conf import settings
156
+ uploads_dir = Path(settings.BASE_DIR).parent / 'storage' / 'uploads'
157
+
158
+ if not uploads_dir.exists():
159
+ return 0
160
+
161
+ cutoff_time = datetime.now().timestamp() - (max_age_hours * 3600)
162
+
163
+ for file_path in uploads_dir.rglob('*'):
164
+ if file_path.is_file():
165
+ try:
166
+ if file_path.stat().st_mtime < cutoff_time:
167
+ file_size = file_path.stat().st_size
168
+ file_path.unlink()
169
+ total_freed += file_size
170
+
171
+ except Exception as e:
172
+ logger.warning(f"Failed to clean upload file {file_path}: {e}")
173
+
174
+ except Exception as e:
175
+ logger.error(f"Upload cleanup failed: {e}")
176
+
177
+ return total_freed
178
+
179
+ def _cleanup_large_logs(self, max_size_mb: int = 50) -> int:
180
+ """Clean up large log files by truncating them."""
181
+ total_freed = 0
182
+
183
+ try:
184
+ from django.conf import settings
185
+ project_root = Path(settings.BASE_DIR).parent
186
+ max_size_bytes = max_size_mb * 1024 * 1024
187
+
188
+ for log_file in project_root.rglob('*.log'):
189
+ try:
190
+ if log_file.stat().st_size > max_size_bytes:
191
+ original_size = log_file.stat().st_size
192
+
193
+ # Truncate the log file
194
+ with open(log_file, 'w') as f:
195
+ f.write(f"# Log truncated at {datetime.now()} due to size limit\n")
196
+
197
+ total_freed += original_size
198
+ logger.info(f"Truncated log {log_file}: {original_size / (1024**2):.1f}MB")
199
+
200
+ except Exception as e:
201
+ logger.warning(f"Failed to truncate log {log_file}: {e}")
202
+
203
+ except Exception as e:
204
+ logger.error(f"Log cleanup failed: {e}")
205
+
206
+ return total_freed
207
+
208
+ def _cleanup_temp_files(self) -> int:
209
+ """Clean up temporary files."""
210
+ total_freed = 0
211
+
212
+ try:
213
+ temp_patterns = [
214
+ '/tmp/tmp*',
215
+ '/tmp/temp*',
216
+ '/tmp/django*',
217
+ '/tmp/ffmpeg*',
218
+ ]
219
+
220
+ for pattern in temp_patterns:
221
+ import glob
222
+ for temp_file in glob.glob(pattern):
223
+ try:
224
+ temp_path = Path(temp_file)
225
+ if temp_path.is_file():
226
+ file_size = temp_path.stat().st_size
227
+ temp_path.unlink()
228
+ total_freed += file_size
229
+
230
+ except Exception as e:
231
+ logger.warning(f"Failed to clean temp file {temp_file}: {e}")
232
+
233
+ except Exception as e:
234
+ logger.error(f"Temp file cleanup failed: {e}")
235
+
236
+ return total_freed
237
+
238
+ def process_video_with_storage_management(
239
+ self,
240
+ video_file: VideoFile,
241
+ cleanup_frames_after: bool = True,
242
+ progress_callback: Optional[callable] = None
243
+ ) -> bool:
244
+ """
245
+ Process a video with automatic storage management.
246
+
247
+ Args:
248
+ video_file: VideoFile instance to process
249
+ cleanup_frames_after: Whether to clean up frames after processing
250
+ progress_callback: Optional progress callback function
251
+
252
+ Returns:
253
+ True if processing succeeded, False otherwise
254
+ """
255
+ try:
256
+ # Estimate required space (rough calculation)
257
+ video_size = 0
258
+ if video_file.raw_file and hasattr(video_file.raw_file, 'size'):
259
+ video_size = video_file.raw_file.size
260
+
261
+ # Estimate: frames ~= 3x video size, processing ~= 2x video size
262
+ estimated_space_needed = video_size * 5
263
+
264
+ # Check storage before starting
265
+ self.check_and_ensure_storage(estimated_space_needed)
266
+
267
+ # Update task status
268
+ task = self._get_or_create_task(video_file)
269
+ task.start_processing()
270
+
271
+ if progress_callback:
272
+ progress_callback(10, "Starting video processing...")
273
+
274
+ # Run the actual video processing pipeline
275
+ success = video_file.pipe_1(
276
+ model_name="image_multilabel_classification_colonoscopy_default",
277
+ delete_frames_after=cleanup_frames_after
278
+ )
279
+
280
+ if success:
281
+ if progress_callback:
282
+ progress_callback(90, "Processing completed, cleaning up...")
283
+
284
+ # Mark as completed
285
+ task.mark_completed("Video processing completed successfully")
286
+
287
+ # Additional cleanup if requested
288
+ if cleanup_frames_after:
289
+ self._cleanup_video_frames(video_file)
290
+
291
+ if progress_callback:
292
+ progress_callback(100, "Processing completed successfully")
293
+
294
+ logger.info(f"Video processing completed successfully: {video_file.uuid}")
295
+ return True
296
+
297
+ task.mark_failed("Video processing pipeline failed")
298
+ logger.error(f"Video processing failed: {video_file.uuid}")
299
+ return False
300
+
301
+ except InsufficientStorageError as e:
302
+ logger.error(f"Storage error during video processing: {e}")
303
+ task = self._get_or_create_task(video_file)
304
+ task.mark_failed(f"Insufficient storage: {e}")
305
+ return False
306
+
307
+ except Exception as e:
308
+ logger.error(f"Video processing failed: {e}")
309
+ task = self._get_or_create_task(video_file)
310
+ task.mark_failed(f"Processing error: {e}")
311
+ return False
312
+
313
+ def _get_or_create_task(self, video_file: VideoFile) -> AnonymizationTask:
314
+ """Get or create an anonymization task for the video."""
315
+ task, created = AnonymizationTask.objects.get_or_create(
316
+ video_file=video_file,
317
+ defaults={
318
+ 'status': 'not_started',
319
+ 'progress': 0,
320
+ 'message': 'Initializing...'
321
+ }
322
+ )
323
+ return task
324
+
325
+ def _cleanup_video_frames(self, video_file: VideoFile):
326
+ """Clean up frames for a specific video."""
327
+ try:
328
+ from django.conf import settings
329
+ frames_dir = Path(settings.BASE_DIR).parent / 'storage' / 'frames'
330
+
331
+ # Find frame directories for this video
332
+ video_frame_dirs = list(frames_dir.glob(f"*{video_file.uuid}*"))
333
+
334
+ for frame_dir in video_frame_dirs:
335
+ if frame_dir.is_dir():
336
+ shutil.rmtree(frame_dir, ignore_errors=True)
337
+ logger.info(f"Cleaned up frames for video {video_file.uuid}")
338
+
339
+ except Exception as e:
340
+ logger.warning(f"Failed to clean up frames for {video_file.uuid}: {e}")
341
+
342
+
343
+ # Global instance for easy access
344
+ storage_aware_processor = StorageAwareVideoProcessor()