endoreg-db 0.3.6__py3-none-any.whl → 0.8.6.1__py3-none-any.whl

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  1. endoreg_db/admin.py +92 -3
  2. endoreg_db/api_urls.py +4 -0
  3. endoreg_db/apps.py +18 -6
  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 +144 -65
  9. endoreg_db/data/ai_model/data.yaml +7 -0
  10. endoreg_db/data/{label → ai_model_label}/label/data.yaml +88 -62
  11. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  12. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  13. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  14. endoreg_db/data/{label → ai_model_label}/label-type/data.yaml +6 -6
  15. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  16. endoreg_db/data/{model_type → ai_model_type}/data.yaml +6 -6
  17. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  18. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  19. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -167
  20. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +7 -7
  21. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +8 -8
  22. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +22 -22
  23. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +18 -18
  24. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +18 -18
  25. endoreg_db/data/case_template/rule/19_create_patient.yaml +16 -16
  26. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -35
  27. endoreg_db/data/case_template/rule_value_type/base_types.yaml +58 -58
  28. endoreg_db/data/case_template/template/base.yaml +7 -7
  29. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +2 -2
  30. endoreg_db/data/case_template/tmp/_rule_value +13 -13
  31. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -21
  32. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +9 -9
  33. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +6 -6
  34. endoreg_db/data/center/data.yaml +90 -59
  35. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -144
  36. endoreg_db/data/center_shift/ukw.yaml +9 -0
  37. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -48
  38. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  39. endoreg_db/data/db_summary.csv +58 -0
  40. endoreg_db/data/db_summary.xlsx +0 -0
  41. endoreg_db/data/disease/cardiovascular.yaml +37 -37
  42. endoreg_db/data/disease/hepatology.yaml +4 -4
  43. endoreg_db/data/disease/misc.yaml +5 -6
  44. endoreg_db/data/disease/renal.yaml +4 -4
  45. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -6
  46. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +5 -5
  47. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -41
  48. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +19 -19
  49. endoreg_db/data/distribution/date/patient.yaml +6 -6
  50. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  51. endoreg_db/data/distribution/single_categorical/patient.yaml +6 -6
  52. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -132
  53. endoreg_db/data/endoscope/data.yaml +93 -0
  54. endoreg_db/data/endoscope_type/data.yaml +10 -10
  55. endoreg_db/data/endoscopy_processor/data.yaml +50 -45
  56. endoreg_db/data/event/cardiology.yaml +15 -28
  57. endoreg_db/data/event/neurology.yaml +13 -13
  58. endoreg_db/data/event/surgery.yaml +12 -12
  59. endoreg_db/data/event/thrombembolism.yaml +19 -19
  60. endoreg_db/data/examination/examinations/data.yaml +72 -66
  61. endoreg_db/data/examination/time/data.yaml +47 -47
  62. endoreg_db/data/examination/time-type/data.yaml +7 -7
  63. endoreg_db/data/examination/type/data.yaml +17 -5
  64. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  65. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  66. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  67. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  68. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  69. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  70. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  71. endoreg_db/data/finding/complication.yaml +16 -0
  72. endoreg_db/data/finding/data.yaml +105 -0
  73. endoreg_db/data/finding/examination_setting.yaml +16 -0
  74. endoreg_db/data/finding/medication_related.yaml +18 -0
  75. endoreg_db/data/finding/outcome.yaml +12 -0
  76. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  77. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  78. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  79. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  80. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  81. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  82. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  83. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  84. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  85. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  87. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  88. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  89. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  90. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  91. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  92. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  93. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  94. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  95. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  96. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  97. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  98. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  99. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  100. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  101. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  105. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  106. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  107. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  108. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  109. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  110. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  111. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  112. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  113. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  114. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  115. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  116. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  117. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  118. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  119. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  120. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  121. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  122. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  123. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  124. endoreg_db/data/finding_type/data.yaml +43 -0
  125. endoreg_db/data/gender/data.yaml +42 -18
  126. endoreg_db/data/information_source/annotation.yaml +6 -0
  127. endoreg_db/data/information_source/data.yaml +30 -30
  128. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  129. endoreg_db/data/information_source/medication.yaml +5 -5
  130. endoreg_db/data/information_source/prediction.yaml +7 -0
  131. endoreg_db/data/information_source_type/data.yaml +8 -0
  132. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -31
  133. endoreg_db/data/lab_value/coagulation.yaml +54 -49
  134. endoreg_db/data/lab_value/electrolytes.yaml +228 -190
  135. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -121
  136. endoreg_db/data/lab_value/hematology.yaml +184 -169
  137. endoreg_db/data/lab_value/hormones.yaml +59 -53
  138. endoreg_db/data/lab_value/lipids.yaml +53 -44
  139. endoreg_db/data/lab_value/misc.yaml +76 -30
  140. endoreg_db/data/lab_value/renal_function.yaml +12 -11
  141. endoreg_db/data/log_type/data.yaml +57 -0
  142. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  143. endoreg_db/data/lx_client_type/base.yaml +30 -0
  144. endoreg_db/data/lx_permission/base.yaml +24 -0
  145. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  146. endoreg_db/data/medication/anticoagulation.yaml +64 -64
  147. endoreg_db/data/medication/tah.yaml +69 -69
  148. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -120
  149. endoreg_db/data/medication_indication_type/data.yaml +10 -10
  150. endoreg_db/data/medication_indication_type/thrombembolism.yaml +40 -40
  151. endoreg_db/data/medication_intake_time/base.yaml +30 -30
  152. endoreg_db/data/medication_schedule/apixaban.yaml +94 -94
  153. endoreg_db/data/medication_schedule/ass.yaml +12 -12
  154. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -26
  155. endoreg_db/data/names_first/first_names.yaml +54 -0
  156. endoreg_db/data/names_last/last_names.yaml +51 -0
  157. endoreg_db/data/network_device/data.yaml +59 -0
  158. endoreg_db/data/network_device_type/data.yaml +12 -0
  159. endoreg_db/data/organ/data.yaml +29 -0
  160. endoreg_db/data/patient_lab_sample_type/generic.yaml +5 -5
  161. endoreg_db/data/pdf_type/data.yaml +46 -28
  162. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
  163. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
  164. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
  165. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
  166. endoreg_db/data/profession/data.yaml +70 -70
  167. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  168. endoreg_db/data/qualification/m2.yaml +39 -0
  169. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  170. endoreg_db/data/qualification/sonography.yaml +36 -0
  171. endoreg_db/data/qualification_type/base.yaml +29 -0
  172. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -55
  173. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  174. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -26
  175. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -19
  176. endoreg_db/data/requirement/age.yaml +26 -0
  177. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  178. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  179. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  180. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  181. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  182. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  183. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  184. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  185. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  186. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  187. endoreg_db/data/requirement/gender.yaml +25 -0
  188. endoreg_db/data/requirement/lab_value.yaml +441 -0
  189. endoreg_db/data/requirement/medication.yaml +93 -0
  190. endoreg_db/data/requirement_operator/age.yaml +13 -0
  191. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  192. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  193. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  194. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  195. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  196. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  197. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  198. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
  199. endoreg_db/data/risk/bleeding.yaml +26 -0
  200. endoreg_db/data/risk/thrombosis.yaml +37 -0
  201. endoreg_db/data/risk_type/data.yaml +27 -0
  202. endoreg_db/data/setup_config.yaml +38 -0
  203. endoreg_db/data/shift/endoscopy.yaml +21 -0
  204. endoreg_db/data/shift/m2.yaml +0 -0
  205. endoreg_db/data/shift_type/base.yaml +35 -0
  206. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  207. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
  208. endoreg_db/data/unit/concentration.yaml +115 -92
  209. endoreg_db/data/unit/data.yaml +17 -17
  210. endoreg_db/data/unit/length.yaml +30 -30
  211. endoreg_db/data/unit/misc.yaml +19 -19
  212. endoreg_db/data/unit/rate.yaml +5 -5
  213. endoreg_db/data/unit/time.yaml +48 -13
  214. endoreg_db/data/unit/volume.yaml +35 -35
  215. endoreg_db/data/unit/weight.yaml +37 -37
  216. endoreg_db/data/waste/data.yaml +11 -11
  217. endoreg_db/exceptions.py +19 -0
  218. endoreg_db/factories/__init__.py +0 -0
  219. endoreg_db/forms/__init__.py +5 -3
  220. endoreg_db/forms/examination_form.py +11 -0
  221. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  222. endoreg_db/forms/patient_form.py +27 -0
  223. endoreg_db/forms/questionnaires/__init__.py +1 -1
  224. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
  225. endoreg_db/forms/settings/__init__.py +8 -8
  226. endoreg_db/forms/unit.py +5 -5
  227. endoreg_db/helpers/__init__.py +0 -0
  228. endoreg_db/helpers/count_db.py +45 -0
  229. endoreg_db/helpers/data_loader.py +208 -0
  230. endoreg_db/helpers/default_objects.py +378 -0
  231. endoreg_db/helpers/download_segmentation_model.py +31 -0
  232. endoreg_db/helpers/interact.py +6 -0
  233. endoreg_db/helpers/test_video_helper.py +119 -0
  234. endoreg_db/logger_conf.py +140 -0
  235. endoreg_db/management/__init__.py +1 -0
  236. endoreg_db/management/commands/__init__.py +1 -0
  237. endoreg_db/management/commands/anonymize_video.py +0 -0
  238. endoreg_db/management/commands/check_auth.py +125 -0
  239. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  240. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  241. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  242. endoreg_db/management/commands/fix_video_paths.py +165 -0
  243. endoreg_db/management/commands/import_fallback_video.py +203 -0
  244. endoreg_db/management/commands/import_report.py +298 -0
  245. endoreg_db/management/commands/import_video.py +423 -0
  246. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  247. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  248. endoreg_db/management/commands/load_ai_model_data.py +77 -45
  249. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  250. endoreg_db/management/commands/load_base_db_data.py +192 -128
  251. endoreg_db/management/commands/load_center_data.py +68 -43
  252. endoreg_db/management/commands/{load_medication_intake_time_data.py → load_contraindication_data.py} +40 -40
  253. endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
  254. endoreg_db/management/commands/load_disease_classification_data.py +40 -40
  255. endoreg_db/management/commands/load_disease_data.py +61 -39
  256. endoreg_db/management/commands/load_distribution_data.py +65 -65
  257. endoreg_db/management/commands/{load_endoscope_type_data.py → load_endoscope_data.py} +67 -44
  258. endoreg_db/management/commands/load_event_data.py +40 -40
  259. endoreg_db/management/commands/load_examination_data.py +74 -74
  260. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  261. endoreg_db/management/commands/load_finding_data.py +128 -0
  262. endoreg_db/management/commands/load_gender_data.py +43 -43
  263. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +131 -132
  264. endoreg_db/management/commands/load_information_source.py +50 -44
  265. endoreg_db/management/commands/load_lab_value_data.py +49 -49
  266. endoreg_db/management/commands/load_medication_data.py +103 -41
  267. endoreg_db/management/commands/load_name_data.py +37 -0
  268. endoreg_db/management/commands/{load_medication_indication_type_data.py → load_organ_data.py} +42 -40
  269. endoreg_db/management/commands/load_pdf_type_data.py +60 -60
  270. endoreg_db/management/commands/load_profession_data.py +43 -43
  271. endoreg_db/management/commands/load_qualification_data.py +59 -0
  272. endoreg_db/management/commands/{load_report_reader_flag.py → load_report_reader_flag_data.py} +45 -45
  273. endoreg_db/management/commands/load_requirement_data.py +180 -0
  274. endoreg_db/management/commands/load_risk_data.py +56 -0
  275. endoreg_db/management/commands/load_shift_data.py +60 -0
  276. endoreg_db/management/commands/load_tag_data.py +57 -0
  277. endoreg_db/management/commands/load_unit_data.py +45 -45
  278. endoreg_db/management/commands/load_user_groups.py +28 -28
  279. endoreg_db/management/commands/register_ai_model.py +64 -65
  280. endoreg_db/management/commands/reset_celery_schedule.py +9 -9
  281. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  282. endoreg_db/management/commands/start_filewatcher.py +106 -0
  283. endoreg_db/management/commands/storage_management.py +548 -0
  284. endoreg_db/management/commands/summarize_db_content.py +189 -0
  285. endoreg_db/management/commands/validate_video.py +204 -0
  286. endoreg_db/management/commands/validate_video_files.py +161 -0
  287. endoreg_db/management/commands/video_validation.py +22 -0
  288. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  289. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  290. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
  291. endoreg_db/mermaid/classification.md +8 -0
  292. endoreg_db/mermaid/examination.md +8 -0
  293. endoreg_db/mermaid/findings.md +7 -0
  294. endoreg_db/mermaid/image_classification.md +28 -0
  295. endoreg_db/mermaid/interventions.md +8 -0
  296. endoreg_db/mermaid/morphology.md +8 -0
  297. endoreg_db/mermaid/patient_creation.md +14 -0
  298. endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
  299. endoreg_db/migrations/0001_initial.py +1857 -582
  300. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  301. endoreg_db/migrations/0003_add_center_display_name.py +30 -0
  302. endoreg_db/models/__init__.py +359 -74
  303. endoreg_db/models/administration/__init__.py +116 -0
  304. endoreg_db/models/administration/ai/__init__.py +9 -0
  305. endoreg_db/models/administration/ai/active_model.py +35 -0
  306. endoreg_db/models/administration/ai/ai_model.py +156 -0
  307. endoreg_db/models/{ai_model → administration/ai}/model_type.py +41 -26
  308. endoreg_db/models/administration/case/__init__.py +19 -0
  309. endoreg_db/models/administration/case/case.py +114 -0
  310. endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +15 -6
  311. endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +125 -81
  312. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +269 -276
  313. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +86 -73
  314. endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +26 -28
  315. endoreg_db/models/{center → administration/center}/__init__.py +13 -4
  316. endoreg_db/models/administration/center/center.py +67 -0
  317. endoreg_db/models/administration/center/center_product.py +64 -0
  318. endoreg_db/models/administration/center/center_resource.py +49 -0
  319. endoreg_db/models/administration/center/center_shift.py +88 -0
  320. endoreg_db/models/administration/center/center_waste.py +30 -0
  321. endoreg_db/models/administration/permissions/__init__.py +44 -0
  322. endoreg_db/models/administration/person/__init__.py +24 -0
  323. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  324. endoreg_db/models/administration/person/employee/employee.py +35 -0
  325. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  326. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  327. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  328. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  329. endoreg_db/models/administration/person/names/__init__.py +0 -0
  330. endoreg_db/models/{persons → administration/person/names}/first_name.py +18 -18
  331. endoreg_db/models/{persons → administration/person/names}/last_name.py +18 -19
  332. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  333. endoreg_db/models/administration/person/patient/patient.py +460 -0
  334. endoreg_db/models/{persons → administration/person}/person.py +31 -31
  335. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  336. endoreg_db/models/administration/person/user/__init__.py +5 -0
  337. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  338. endoreg_db/models/administration/product/__init__.py +14 -0
  339. endoreg_db/models/administration/product/product.py +97 -0
  340. endoreg_db/models/administration/product/product_group.py +39 -0
  341. endoreg_db/models/administration/product/product_material.py +54 -0
  342. endoreg_db/models/{product → administration/product}/product_weight.py +47 -26
  343. endoreg_db/models/{product → administration/product}/reference_product.py +130 -99
  344. endoreg_db/models/administration/qualification/__init__.py +7 -0
  345. endoreg_db/models/administration/qualification/qualification.py +37 -0
  346. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  347. endoreg_db/models/administration/shift/__init__.py +9 -0
  348. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  349. endoreg_db/models/administration/shift/shift.py +51 -0
  350. endoreg_db/models/administration/shift/shift_type.py +108 -0
  351. endoreg_db/models/label/__init__.py +24 -1
  352. endoreg_db/models/label/annotation/__init__.py +12 -0
  353. endoreg_db/models/label/annotation/image_classification.py +84 -0
  354. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  355. endoreg_db/models/label/label.py +83 -84
  356. endoreg_db/models/label/label_set.py +53 -0
  357. endoreg_db/models/label/label_type.py +29 -0
  358. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  359. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  360. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  361. endoreg_db/models/label/video_segmentation_label.py +31 -0
  362. endoreg_db/models/label/video_segmentation_labelset.py +27 -0
  363. endoreg_db/models/media/__init__.py +16 -0
  364. endoreg_db/models/media/frame/__init__.py +3 -0
  365. endoreg_db/models/media/frame/frame.py +111 -0
  366. endoreg_db/models/media/pdf/__init__.py +11 -0
  367. endoreg_db/models/media/pdf/raw_pdf.py +757 -0
  368. endoreg_db/models/media/pdf/report_file.py +162 -0
  369. endoreg_db/models/media/pdf/report_reader/__init__.py +7 -0
  370. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  371. endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +19 -19
  372. endoreg_db/models/media/video/__init__.py +8 -0
  373. endoreg_db/models/media/video/create_from_file.py +358 -0
  374. endoreg_db/models/media/video/pipe_1.py +213 -0
  375. endoreg_db/models/media/video/pipe_2.py +105 -0
  376. endoreg_db/models/media/video/refactor_plan.md +0 -0
  377. endoreg_db/models/media/video/video_file.py +825 -0
  378. endoreg_db/models/media/video/video_file_ai.py +443 -0
  379. endoreg_db/models/media/video/video_file_anonymize.py +349 -0
  380. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  381. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  382. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  383. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  384. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  385. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  386. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  387. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  388. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  389. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  390. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  391. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  392. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +141 -0
  393. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  394. endoreg_db/models/media/video/video_file_frames.py +0 -0
  395. endoreg_db/models/media/video/video_file_io.py +168 -0
  396. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  397. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  398. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  399. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  400. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  401. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  402. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  403. endoreg_db/models/media/video/video_file_segments.py +209 -0
  404. endoreg_db/models/media/video/video_metadata.py +65 -0
  405. endoreg_db/models/media/video/video_processing.py +152 -0
  406. endoreg_db/models/medical/__init__.py +146 -0
  407. endoreg_db/models/medical/contraindication/__init__.py +17 -0
  408. endoreg_db/models/medical/disease.py +156 -0
  409. endoreg_db/models/medical/event.py +137 -0
  410. endoreg_db/models/medical/examination/__init__.py +9 -0
  411. endoreg_db/models/medical/examination/examination.py +148 -0
  412. endoreg_db/models/medical/examination/examination_indication.py +278 -0
  413. endoreg_db/models/medical/examination/examination_time.py +49 -0
  414. endoreg_db/models/medical/examination/examination_time_type.py +41 -0
  415. endoreg_db/models/medical/examination/examination_type.py +48 -0
  416. endoreg_db/models/medical/finding/__init__.py +18 -0
  417. endoreg_db/models/medical/finding/finding.py +96 -0
  418. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  419. endoreg_db/models/medical/finding/finding_intervention.py +52 -0
  420. endoreg_db/models/medical/finding/finding_type.py +35 -0
  421. endoreg_db/models/medical/hardware/__init__.py +8 -0
  422. endoreg_db/models/medical/hardware/endoscope.py +65 -0
  423. endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +182 -143
  424. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  425. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  426. endoreg_db/models/medical/medication/__init__.py +19 -0
  427. endoreg_db/models/medical/medication/medication.py +31 -0
  428. endoreg_db/models/medical/medication/medication_indication.py +50 -0
  429. endoreg_db/models/medical/medication/medication_indication_type.py +39 -0
  430. endoreg_db/models/medical/medication/medication_intake_time.py +44 -0
  431. endoreg_db/models/medical/medication/medication_schedule.py +45 -0
  432. endoreg_db/models/medical/organ/__init__.py +35 -0
  433. endoreg_db/models/medical/patient/__init__.py +56 -0
  434. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  435. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  436. endoreg_db/models/medical/patient/patient_event.py +75 -0
  437. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  438. endoreg_db/models/medical/patient/patient_examination_indication.py +44 -0
  439. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  440. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  441. endoreg_db/models/medical/patient/patient_finding_intervention.py +40 -0
  442. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  443. endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +222 -176
  444. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  445. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  446. endoreg_db/models/medical/risk/__init__.py +7 -0
  447. endoreg_db/models/medical/risk/risk.py +72 -0
  448. endoreg_db/models/medical/risk/risk_type.py +51 -0
  449. endoreg_db/models/metadata/__init__.py +19 -0
  450. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  451. endoreg_db/models/metadata/model_meta.py +206 -0
  452. endoreg_db/models/metadata/model_meta_logic.py +343 -0
  453. endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +89 -70
  454. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  455. endoreg_db/models/metadata/sensitive_meta_logic.py +1048 -0
  456. endoreg_db/models/metadata/video_meta.py +332 -0
  457. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  458. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  459. endoreg_db/models/other/__init__.py +40 -5
  460. endoreg_db/models/other/distribution/__init__.py +44 -0
  461. endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
  462. endoreg_db/models/other/distribution/date_value_distribution.py +89 -0
  463. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
  464. endoreg_db/models/other/distribution/numeric_value_distribution.py +125 -0
  465. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
  466. endoreg_db/models/other/emission/__init__.py +5 -0
  467. endoreg_db/models/other/emission/emission_factor.py +94 -0
  468. endoreg_db/models/{persons → other}/gender.py +27 -22
  469. endoreg_db/models/other/information_source.py +159 -0
  470. endoreg_db/models/other/material.py +28 -16
  471. endoreg_db/models/other/resource.py +21 -17
  472. endoreg_db/models/other/tag.py +27 -0
  473. endoreg_db/models/other/transport_route.py +33 -21
  474. endoreg_db/models/{unit.py → other/unit.py} +32 -22
  475. endoreg_db/models/other/waste.py +27 -20
  476. endoreg_db/models/requirement/__init__.py +11 -0
  477. endoreg_db/models/requirement/requirement.py +767 -0
  478. endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
  479. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  480. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  481. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +95 -0
  482. endoreg_db/models/requirement/requirement_operator.py +176 -0
  483. endoreg_db/models/requirement/requirement_set.py +287 -0
  484. endoreg_db/models/rule/__init__.py +13 -0
  485. endoreg_db/models/{rules → rule}/rule.py +27 -24
  486. endoreg_db/models/{rules → rule}/rule_applicator.py +224 -224
  487. endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +16 -18
  488. endoreg_db/models/{rules → rule}/rule_type.py +19 -21
  489. endoreg_db/models/{rules → rule}/ruleset.py +17 -19
  490. endoreg_db/models/state/__init__.py +12 -0
  491. endoreg_db/models/state/abstract.py +11 -0
  492. endoreg_db/models/state/audit_ledger.py +150 -0
  493. endoreg_db/models/state/label_video_segment.py +22 -0
  494. endoreg_db/models/state/raw_pdf.py +187 -0
  495. endoreg_db/models/state/sensitive_meta.py +46 -0
  496. endoreg_db/models/state/video.py +232 -0
  497. endoreg_db/models/upload_job.py +99 -0
  498. endoreg_db/models/utils.py +135 -0
  499. endoreg_db/queries/__init__.py +4 -4
  500. endoreg_db/queries/annotations/__init__.py +2 -2
  501. endoreg_db/queries/annotations/legacy.py +158 -159
  502. endoreg_db/renames.yml +8 -0
  503. endoreg_db/root_urls.py +9 -0
  504. endoreg_db/schemas/__init__.py +0 -0
  505. endoreg_db/schemas/examination_evaluation.py +27 -0
  506. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  507. endoreg_db/serializers/__init__.py +118 -10
  508. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +223 -0
  509. endoreg_db/serializers/_old/raw_video_meta_validation.py +179 -0
  510. endoreg_db/serializers/_old/video.py +71 -0
  511. endoreg_db/serializers/administration/__init__.py +14 -0
  512. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  513. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  514. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  515. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  516. endoreg_db/serializers/administration/center.py +9 -0
  517. endoreg_db/serializers/administration/gender.py +9 -0
  518. endoreg_db/serializers/anonymization.py +69 -0
  519. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  520. endoreg_db/serializers/examination/__init__.py +10 -0
  521. endoreg_db/serializers/examination/base.py +46 -0
  522. endoreg_db/serializers/examination/dropdown.py +21 -0
  523. endoreg_db/serializers/examination_serializer.py +12 -0
  524. endoreg_db/serializers/finding/__init__.py +5 -0
  525. endoreg_db/serializers/finding/finding.py +54 -0
  526. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  527. endoreg_db/serializers/finding_classification/choice.py +19 -0
  528. endoreg_db/serializers/finding_classification/classification.py +13 -0
  529. endoreg_db/serializers/label/__init__.py +7 -0
  530. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  531. endoreg_db/serializers/label/label.py +15 -0
  532. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  533. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  534. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  535. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  536. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  537. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  538. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  539. endoreg_db/serializers/meta/__init__.py +19 -0
  540. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  541. endoreg_db/serializers/meta/report_meta.py +53 -0
  542. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  543. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  544. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  545. endoreg_db/serializers/meta/video_meta.py +39 -0
  546. endoreg_db/serializers/misc/__init__.py +14 -0
  547. endoreg_db/serializers/misc/file_overview.py +182 -0
  548. endoreg_db/serializers/misc/sensitive_patient_data.py +120 -0
  549. endoreg_db/serializers/misc/stats.py +33 -0
  550. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  551. endoreg_db/serializers/misc/upload_job.py +71 -0
  552. endoreg_db/serializers/patient/__init__.py +11 -0
  553. endoreg_db/serializers/patient/patient.py +86 -0
  554. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  555. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  556. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  557. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  558. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  559. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  560. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  561. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  562. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  563. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  564. endoreg_db/serializers/pdf/__init__.py +5 -0
  565. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  566. endoreg_db/serializers/report/__init__.py +9 -0
  567. endoreg_db/serializers/report/mixins.py +45 -0
  568. endoreg_db/serializers/report/report.py +105 -0
  569. endoreg_db/serializers/report/report_list.py +22 -0
  570. endoreg_db/serializers/report/secure_file_url.py +26 -0
  571. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  572. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  573. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  574. endoreg_db/serializers/video/__init__.py +7 -0
  575. endoreg_db/serializers/video/segmentation.py +263 -0
  576. endoreg_db/serializers/video/video_file_brief.py +10 -0
  577. endoreg_db/serializers/video/video_file_detail.py +83 -0
  578. endoreg_db/serializers/video/video_file_list.py +67 -0
  579. endoreg_db/serializers/video/video_metadata.py +105 -0
  580. endoreg_db/serializers/video/video_processing_history.py +153 -0
  581. endoreg_db/serializers/video_examination.py +198 -0
  582. endoreg_db/services/__init__.py +5 -0
  583. endoreg_db/services/anonymization.py +223 -0
  584. endoreg_db/services/examination_evaluation.py +149 -0
  585. endoreg_db/services/finding_description_service.py +0 -0
  586. endoreg_db/services/lookup_service.py +411 -0
  587. endoreg_db/services/lookup_store.py +266 -0
  588. endoreg_db/services/pdf_import.py +1382 -0
  589. endoreg_db/services/polling_coordinator.py +288 -0
  590. endoreg_db/services/pseudonym_service.py +89 -0
  591. endoreg_db/services/requirements_object.py +147 -0
  592. endoreg_db/services/segment_sync.py +155 -0
  593. endoreg_db/services/storage_aware_video_processor.py +344 -0
  594. endoreg_db/services/video_import.py +1259 -0
  595. endoreg_db/tasks/upload_tasks.py +207 -0
  596. endoreg_db/tasks/video_ingest.py +157 -0
  597. endoreg_db/tasks/video_processing_tasks.py +327 -0
  598. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  599. endoreg_db/templates/admin/start_examination.html +12 -0
  600. endoreg_db/templates/timeline.html +176 -0
  601. endoreg_db/urls/__init__.py +83 -0
  602. endoreg_db/urls/anonymization.py +32 -0
  603. endoreg_db/urls/auth.py +16 -0
  604. endoreg_db/urls/classification.py +39 -0
  605. endoreg_db/urls/examination.py +54 -0
  606. endoreg_db/urls/files.py +6 -0
  607. endoreg_db/urls/label_video_segment_validate.py +33 -0
  608. endoreg_db/urls/label_video_segments.py +46 -0
  609. endoreg_db/urls/media.py +227 -0
  610. endoreg_db/urls/patient.py +19 -0
  611. endoreg_db/urls/report.py +48 -0
  612. endoreg_db/urls/requirements.py +13 -0
  613. endoreg_db/urls/sensitive_meta.py +0 -0
  614. endoreg_db/urls/stats.py +46 -0
  615. endoreg_db/urls/upload.py +20 -0
  616. endoreg_db/urls/video.py +61 -0
  617. endoreg_db/urls.py +9 -0
  618. endoreg_db/utils/__init__.py +88 -1
  619. endoreg_db/utils/ai/__init__.py +9 -0
  620. endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +5 -8
  621. endoreg_db/utils/ai/inference_dataset.py +52 -0
  622. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  623. endoreg_db/utils/ai/postprocess.py +63 -0
  624. endoreg_db/utils/ai/predict.py +291 -0
  625. endoreg_db/utils/ai/preprocess.py +68 -0
  626. endoreg_db/utils/calc_duration_seconds.py +24 -0
  627. endoreg_db/utils/case_generator/__init__.py +0 -0
  628. endoreg_db/utils/case_generator/case_generator.py +159 -0
  629. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  630. endoreg_db/utils/case_generator/utils.py +30 -0
  631. endoreg_db/utils/check_video_files.py +148 -0
  632. endoreg_db/utils/cropping.py +28 -28
  633. endoreg_db/utils/dataloader.py +175 -92
  634. endoreg_db/utils/dates.py +60 -0
  635. endoreg_db/utils/env.py +33 -0
  636. endoreg_db/utils/extract_specific_frames.py +72 -0
  637. endoreg_db/utils/file_operations.py +58 -30
  638. endoreg_db/utils/fix_video_path_direct.py +141 -0
  639. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  640. endoreg_db/utils/hashs.py +153 -34
  641. endoreg_db/utils/links/__init__.py +0 -0
  642. endoreg_db/utils/links/requirement_link.py +193 -0
  643. endoreg_db/utils/mime_types.py +0 -0
  644. endoreg_db/utils/names.py +76 -0
  645. endoreg_db/utils/ocr.py +190 -197
  646. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  647. endoreg_db/utils/paths.py +95 -0
  648. endoreg_db/utils/permissions.py +143 -0
  649. endoreg_db/utils/pipelines/Readme.md +235 -0
  650. endoreg_db/utils/pipelines/__init__.py +0 -0
  651. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  652. endoreg_db/utils/product/__init__.py +0 -0
  653. endoreg_db/utils/product/sum_emissions.py +20 -0
  654. endoreg_db/utils/product/sum_weights.py +18 -0
  655. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  656. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  657. endoreg_db/utils/requirement_helpers.py +0 -0
  658. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  659. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  660. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  661. endoreg_db/utils/setup_config.py +177 -0
  662. endoreg_db/utils/translation.py +27 -0
  663. endoreg_db/utils/uuid.py +4 -4
  664. endoreg_db/utils/validate_endo_roi.py +19 -0
  665. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  666. endoreg_db/utils/validate_video_detailed.py +357 -0
  667. endoreg_db/utils/video/__init__.py +26 -0
  668. endoreg_db/utils/video/extract_frames.py +88 -0
  669. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  670. endoreg_db/utils/video/names.py +42 -0
  671. endoreg_db/utils/video/streaming_processor.py +312 -0
  672. endoreg_db/utils/video/video_splitter.py +94 -0
  673. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  674. endoreg_db/views/__init__.py +275 -0
  675. endoreg_db/views/anonymization/__init__.py +27 -0
  676. endoreg_db/views/anonymization/media_management.py +454 -0
  677. endoreg_db/views/anonymization/overview.py +216 -0
  678. endoreg_db/views/anonymization/validate.py +107 -0
  679. endoreg_db/views/auth/__init__.py +13 -0
  680. endoreg_db/views/auth/keycloak.py +113 -0
  681. endoreg_db/views/examination/__init__.py +33 -0
  682. endoreg_db/views/examination/examination.py +37 -0
  683. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  684. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  685. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  686. endoreg_db/views/examination/get_findings.py +41 -0
  687. endoreg_db/views/examination/get_instruments.py +18 -0
  688. endoreg_db/views/examination/get_interventions.py +14 -0
  689. endoreg_db/views/finding/__init__.py +9 -0
  690. endoreg_db/views/finding/finding.py +112 -0
  691. endoreg_db/views/finding/get_classifications.py +14 -0
  692. endoreg_db/views/finding/get_interventions.py +17 -0
  693. endoreg_db/views/finding_classification/__init__.py +13 -0
  694. endoreg_db/views/finding_classification/base.py +0 -0
  695. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  696. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  697. endoreg_db/views/label/__init__.py +5 -0
  698. endoreg_db/views/label/label.py +15 -0
  699. endoreg_db/views/label_video_segment/__init__.py +16 -0
  700. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  701. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  702. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  703. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  704. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  705. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  706. endoreg_db/views/label_video_segment/validate.py +226 -0
  707. endoreg_db/views/media/__init__.py +45 -0
  708. endoreg_db/views/media/pdf_media.py +388 -0
  709. endoreg_db/views/media/segments.py +71 -0
  710. endoreg_db/views/media/sensitive_metadata.py +314 -0
  711. endoreg_db/views/media/video_media.py +272 -0
  712. endoreg_db/views/media/video_segments.py +524 -0
  713. endoreg_db/views/meta/__init__.py +15 -0
  714. endoreg_db/views/meta/available_files_list.py +146 -0
  715. endoreg_db/views/meta/report_meta.py +53 -0
  716. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  717. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  718. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  719. endoreg_db/views/misc/__init__.py +63 -0
  720. endoreg_db/views/misc/center.py +13 -0
  721. endoreg_db/views/misc/csrf.py +7 -0
  722. endoreg_db/views/misc/gender.py +14 -0
  723. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  724. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  725. endoreg_db/views/misc/secure_url_validate.py +79 -0
  726. endoreg_db/views/misc/stats.py +220 -0
  727. endoreg_db/views/misc/translation.py +182 -0
  728. endoreg_db/views/misc/upload_views.py +240 -0
  729. endoreg_db/views/patient/__init__.py +5 -0
  730. endoreg_db/views/patient/patient.py +210 -0
  731. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  732. endoreg_db/views/patient_examination/__init__.py +11 -0
  733. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  734. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  735. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  736. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  737. endoreg_db/views/patient_examination/video.py +194 -0
  738. endoreg_db/views/patient_finding/__init__.py +7 -0
  739. endoreg_db/views/patient_finding/base.py +0 -0
  740. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  741. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  742. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  743. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  744. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  745. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  746. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  747. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  748. endoreg_db/views/pdf/__init__.py +8 -0
  749. endoreg_db/views/pdf/pdf_stream.py +187 -0
  750. endoreg_db/views/pdf/reimport.py +177 -0
  751. endoreg_db/views/report/__init__.py +9 -0
  752. endoreg_db/views/report/report_list.py +112 -0
  753. endoreg_db/views/report/report_with_secure_url.py +28 -0
  754. endoreg_db/views/report/start_examination.py +7 -0
  755. endoreg_db/views/requirement/__init__.py +10 -0
  756. endoreg_db/views/requirement/evaluate.py +279 -0
  757. endoreg_db/views/requirement/lookup.py +367 -0
  758. endoreg_db/views/requirement/lookup_store.py +252 -0
  759. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  760. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  761. endoreg_db/views/stats/__init__.py +13 -0
  762. endoreg_db/views/stats/stats_views.py +229 -0
  763. endoreg_db/views/video/__init__.py +59 -0
  764. endoreg_db/views/video/correction.py +530 -0
  765. endoreg_db/views/video/reimport.py +195 -0
  766. endoreg_db/views/video/segmentation.py +274 -0
  767. endoreg_db/views/video/task_status.py +49 -0
  768. endoreg_db/views/video/timeline.py +46 -0
  769. endoreg_db/views/video/video_analyze.py +52 -0
  770. endoreg_db/views/video/video_apply_mask.py +48 -0
  771. endoreg_db/views/video/video_correction.py +21 -0
  772. endoreg_db/views/video/video_download_processed.py +58 -0
  773. endoreg_db/views/video/video_examination_viewset.py +242 -0
  774. endoreg_db/views/video/video_meta.py +29 -0
  775. endoreg_db/views/video/video_processing_history.py +24 -0
  776. endoreg_db/views/video/video_remove_frames.py +48 -0
  777. endoreg_db/views/video/video_stream.py +306 -0
  778. endoreg_db/views.py +0 -3
  779. endoreg_db-0.8.6.1.dist-info/METADATA +383 -0
  780. endoreg_db-0.8.6.1.dist-info/RECORD +793 -0
  781. {endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info}/WHEEL +1 -1
  782. {endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info/licenses}/LICENSE +674 -674
  783. endoreg_db/data/active_model/data.yaml +0 -3
  784. endoreg_db/data/label/label-set/data.yaml +0 -18
  785. endoreg_db/management/commands/_load_model_template.py +0 -41
  786. endoreg_db/management/commands/delete_all.py +0 -18
  787. endoreg_db/management/commands/delete_legacy_images.py +0 -19
  788. endoreg_db/management/commands/delete_legacy_videos.py +0 -17
  789. endoreg_db/management/commands/extract_legacy_video_frames.py +0 -18
  790. endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
  791. endoreg_db/management/commands/fix_auth_permission.py +0 -20
  792. endoreg_db/management/commands/import_legacy_images.py +0 -94
  793. endoreg_db/management/commands/import_legacy_videos.py +0 -76
  794. endoreg_db/management/commands/load_active_model_data.py +0 -45
  795. endoreg_db/management/commands/load_endoscopy_processor_data.py +0 -45
  796. endoreg_db/management/commands/load_g_play_data.py +0 -113
  797. endoreg_db/management/commands/load_label_data.py +0 -67
  798. endoreg_db/management/commands/load_medication_indication_data.py +0 -63
  799. endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
  800. endoreg_db/migrations/0002_rawvideofile.py +0 -26
  801. endoreg_db/migrations/0003_rawvideofile_frames_required.py +0 -18
  802. endoreg_db/migrations/0004_rename_hash_rawvideofile_video_hash.py +0 -18
  803. endoreg_db/migrations/0005_ffmpegmeta_remove_videoimportmeta_center_and_more.py +0 -56
  804. endoreg_db/migrations/0006_rawvideofile_center_alter_videometa_processor.py +0 -25
  805. endoreg_db/migrations/0007_rawvideofile_processor.py +0 -19
  806. endoreg_db/migrations/0008_rename_frames_required_rawvideofile_state_frames_required.py +0 -18
  807. endoreg_db/migrations/0009_sensitivemeta_rawvideofile_sensitive_meta.py +0 -31
  808. endoreg_db/migrations/0010_rename_endoscope_serial_number_sensitivemeta_endoscope_sn.py +0 -18
  809. endoreg_db/migrations/0011_rawvideofile_state_sensitive_data_retrieved.py +0 -18
  810. endoreg_db/migrations/0012_rawvideofile_prediction_dir_and_more.py +0 -109
  811. endoreg_db/migrations/0013_rawpdffile.py +0 -31
  812. endoreg_db/migrations/0014_pdftype_alter_rawpdffile_file_pdfmeta.py +0 -38
  813. endoreg_db/migrations/0015_rename_report_processed_rawpdffile_state_report_processed_and_more.py +0 -31
  814. endoreg_db/migrations/0016_rawpdffile_state_report_processing_required.py +0 -18
  815. endoreg_db/migrations/0017_firstname_lastname_center_first_names_and_more.py +0 -37
  816. endoreg_db/migrations/0018_reportreaderflag_reportreaderconfig.py +0 -37
  817. endoreg_db/migrations/0019_pdftype_cut_off_above_lines_and_more.py +0 -42
  818. endoreg_db/migrations/0020_rename_endoscopy_info_line_pdftype_endoscope_info_line.py +0 -18
  819. endoreg_db/migrations/0021_alter_pdftype_endoscope_info_line.py +0 -19
  820. endoreg_db/migrations/0022_alter_pdftype_endoscope_info_line.py +0 -19
  821. endoreg_db/migrations/0023_ttoquestionnaire_alter_pdftype_endoscope_info_line.py +0 -59
  822. endoreg_db/migrations/0024_remove_ttoquestionnaire_infections_and_more.py +0 -27
  823. endoreg_db/migrations/0025_event_alter_rawpdffile_file_patientevent.py +0 -42
  824. endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py +0 -166
  825. endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py +0 -38
  826. endoreg_db/migrations/0028_alter_unit_abbreviation.py +0 -18
  827. endoreg_db/migrations/0029_medicationintaketime_and_more.py +0 -75
  828. endoreg_db/migrations/0030_medicationindicationtype_and_more.py +0 -101
  829. endoreg_db/migrations/0031_rename_adapt_to_liver_function_medication_adapt_to_age_and_more.py +0 -38
  830. endoreg_db/migrations/0032_alter_medicationschedule_therapy_duration_d.py +0 -18
  831. endoreg_db/migrations/0033_medicationindication_sources.py +0 -18
  832. endoreg_db/migrations/0034_alter_rawpdffile_file.py +0 -20
  833. endoreg_db/migrations/0035_alter_medicationindication_sources.py +0 -18
  834. endoreg_db/migrations/0036_alter_rawpdffile_file.py +0 -20
  835. endoreg_db/migrations/0037_alter_medicationindication_sources.py +0 -18
  836. endoreg_db/migrations/0038_emissionfactor_material_product_productgroup_and_more.py +0 -164
  837. endoreg_db/migrations/0039_referenceproduct_name.py +0 -19
  838. endoreg_db/migrations/0040_quizanswertype_quizquestiontype_quizquestion_and_more.py +0 -50
  839. endoreg_db/migrations/0041_gender_patientmedication_medication_indication_and_more.py +0 -40
  840. endoreg_db/migrations/0042_casetemplateruletype_casetemplaterulevalue_and_more.py +0 -74
  841. endoreg_db/migrations/0043_casetemplatetype_name_de_casetemplatetype_name_en.py +0 -23
  842. endoreg_db/migrations/0044_casetemplateruletype_name_de_and_more.py +0 -23
  843. endoreg_db/migrations/0045_casetemplaterulevalue_value_type.py +0 -19
  844. endoreg_db/migrations/0046_casetemplaterulevalue_target_field.py +0 -18
  845. endoreg_db/migrations/0047_casetemplaterule_target_model.py +0 -18
  846. endoreg_db/migrations/0048_remove_casetemplaterule_chained_rules_and_more.py +0 -22
  847. endoreg_db/migrations/0049_remove_casetemplaterule_rule_values.py +0 -17
  848. endoreg_db/migrations/0050_casetemplaterule_rule_values.py +0 -18
  849. endoreg_db/migrations/0051_remove_casetemplaterule_calling_rules_and_more.py +0 -27
  850. endoreg_db/migrations/0052_rename_case_template_type_casetemplate_template_type.py +0 -18
  851. endoreg_db/migrations/0053_patientlabsampletype_patientlabsample_and_more.py +0 -38
  852. endoreg_db/migrations/0054_multiplecategoricalvaluedistribution_and_more.py +0 -69
  853. endoreg_db/migrations/0055_remove_casetemplaterule_rule_values_and_more.py +0 -59
  854. endoreg_db/migrations/0056_datevaluedistribution_and_more.py +0 -32
  855. endoreg_db/migrations/0057_remove_datevaluedistribution_max_date_and_more.py +0 -72
  856. endoreg_db/migrations/0058_datevaluedistribution_description_and_more.py +0 -28
  857. endoreg_db/migrations/0059_casetemplaterule_rule_values.py +0 -18
  858. endoreg_db/migrations/0060_labvalue__default_date_value_distribution_and_more.py +0 -44
  859. endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py +0 -24
  860. endoreg_db/migrations/0062_labvalue_numeric_precision.py +0 -18
  861. endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py +0 -18
  862. endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py +0 -23
  863. endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py +0 -58
  864. endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py +0 -29
  865. endoreg_db/migrations/0067_alter_medicationindication_indication_type.py +0 -19
  866. endoreg_db/models/ai_model/__init__.py +0 -3
  867. endoreg_db/models/ai_model/active_model.py +0 -9
  868. endoreg_db/models/ai_model/model_meta.py +0 -24
  869. endoreg_db/models/annotation/__init__.py +0 -2
  870. endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -80
  871. endoreg_db/models/annotation/image_classification.py +0 -27
  872. endoreg_db/models/center/center.py +0 -25
  873. endoreg_db/models/center/center_product.py +0 -34
  874. endoreg_db/models/center/center_resource.py +0 -19
  875. endoreg_db/models/center/center_waste.py +0 -11
  876. endoreg_db/models/data_file/__init__.py +0 -6
  877. endoreg_db/models/data_file/base_classes/__init__.py +0 -2
  878. endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -51
  879. endoreg_db/models/data_file/base_classes/abstract_video.py +0 -201
  880. endoreg_db/models/data_file/frame.py +0 -45
  881. endoreg_db/models/data_file/import_classes/__init__.py +0 -32
  882. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
  883. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
  884. endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
  885. endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -188
  886. endoreg_db/models/data_file/import_classes/raw_video.py +0 -343
  887. endoreg_db/models/data_file/metadata/__init__.py +0 -3
  888. endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -31
  889. endoreg_db/models/data_file/metadata/video_meta.py +0 -133
  890. endoreg_db/models/data_file/report_file.py +0 -89
  891. endoreg_db/models/data_file/video/__init__.py +0 -7
  892. endoreg_db/models/data_file/video/import_meta.py +0 -25
  893. endoreg_db/models/data_file/video/video.py +0 -25
  894. endoreg_db/models/data_file/video_segment.py +0 -107
  895. endoreg_db/models/disease.py +0 -56
  896. endoreg_db/models/emission/__init__.py +0 -1
  897. endoreg_db/models/emission/emission_factor.py +0 -20
  898. endoreg_db/models/event.py +0 -22
  899. endoreg_db/models/examination/__init__.py +0 -4
  900. endoreg_db/models/examination/examination.py +0 -26
  901. endoreg_db/models/examination/examination_time.py +0 -27
  902. endoreg_db/models/examination/examination_time_type.py +0 -24
  903. endoreg_db/models/examination/examination_type.py +0 -18
  904. endoreg_db/models/hardware/__init__.py +0 -2
  905. endoreg_db/models/hardware/endoscope.py +0 -44
  906. endoreg_db/models/information_source.py +0 -29
  907. endoreg_db/models/laboratory/__init__.py +0 -1
  908. endoreg_db/models/laboratory/lab_value.py +0 -102
  909. endoreg_db/models/legacy_data/__init__.py +0 -3
  910. endoreg_db/models/legacy_data/image.py +0 -34
  911. endoreg_db/models/medication/__init__.py +0 -1
  912. endoreg_db/models/medication/medication.py +0 -148
  913. endoreg_db/models/other/distribution.py +0 -215
  914. endoreg_db/models/patient_examination/__init__.py +0 -35
  915. endoreg_db/models/permissions/__init__.py +0 -44
  916. endoreg_db/models/persons/__init__.py +0 -7
  917. endoreg_db/models/persons/examiner/__init__.py +0 -2
  918. endoreg_db/models/persons/examiner/examiner.py +0 -16
  919. endoreg_db/models/persons/examiner/examiner_type.py +0 -2
  920. endoreg_db/models/persons/patient/__init__.py +0 -8
  921. endoreg_db/models/persons/patient/case/case.py +0 -30
  922. endoreg_db/models/persons/patient/patient.py +0 -216
  923. endoreg_db/models/persons/patient/patient_disease.py +0 -16
  924. endoreg_db/models/persons/patient/patient_event.py +0 -22
  925. endoreg_db/models/persons/patient/patient_lab_sample.py +0 -106
  926. endoreg_db/models/persons/patient/patient_medication.py +0 -44
  927. endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -28
  928. endoreg_db/models/persons/portal_user_information.py +0 -27
  929. endoreg_db/models/prediction/__init__.py +0 -2
  930. endoreg_db/models/prediction/image_classification.py +0 -37
  931. endoreg_db/models/prediction/video_prediction_meta.py +0 -244
  932. endoreg_db/models/product/__init__.py +0 -5
  933. endoreg_db/models/product/product.py +0 -97
  934. endoreg_db/models/product/product_group.py +0 -19
  935. endoreg_db/models/product/product_material.py +0 -24
  936. endoreg_db/models/questionnaires/__init__.py +0 -114
  937. endoreg_db/models/quiz/__init__.py +0 -2
  938. endoreg_db/models/quiz/quiz_answer.py +0 -41
  939. endoreg_db/models/quiz/quiz_question.py +0 -54
  940. endoreg_db/models/report_reader/__init__.py +0 -2
  941. endoreg_db/models/report_reader/report_reader_config.py +0 -53
  942. endoreg_db/models/rules/__init__.py +0 -5
  943. endoreg_db/queries/get/__init__.py +0 -6
  944. endoreg_db/queries/get/center.py +0 -42
  945. endoreg_db/queries/get/model.py +0 -13
  946. endoreg_db/queries/get/patient.py +0 -14
  947. endoreg_db/queries/get/patient_examination.py +0 -20
  948. endoreg_db/queries/get/report_file.py +0 -33
  949. endoreg_db/queries/get/video.py +0 -31
  950. endoreg_db/serializers/ai_model.py +0 -19
  951. endoreg_db/serializers/annotation.py +0 -17
  952. endoreg_db/serializers/center.py +0 -11
  953. endoreg_db/serializers/examination.py +0 -33
  954. endoreg_db/serializers/frame.py +0 -13
  955. endoreg_db/serializers/hardware.py +0 -21
  956. endoreg_db/serializers/label.py +0 -22
  957. endoreg_db/serializers/patient.py +0 -10
  958. endoreg_db/serializers/prediction.py +0 -15
  959. endoreg_db/serializers/report_file.py +0 -7
  960. endoreg_db/serializers/video.py +0 -27
  961. endoreg_db/tests.py +0 -3
  962. endoreg_db/utils/legacy_ocr.py +0 -201
  963. endoreg_db/utils/video_metadata.py +0 -87
  964. endoreg_db-0.3.6.dist-info/METADATA +0 -33
  965. endoreg_db-0.3.6.dist-info/RECORD +0 -357
  966. /endoreg_db/{models/persons/patient/case/__init__.py → api/serializers/finding_descriptions.py} +0 -0
  967. /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
  968. /endoreg_db/{queries/get/prediction.py → config/__init__.py} +0 -0
  969. /endoreg_db/{queries/get/video_import_meta.py → data/case_template/rule_value/.init} +0 -0
  970. /endoreg_db/{queries/get/video_prediction_meta.py → data/distribution/multiple_categorical/.init} +0 -0
@@ -0,0 +1,548 @@
1
+ import os
2
+ import shutil
3
+ import logging
4
+ from pathlib import Path
5
+ from datetime import datetime, timedelta
6
+ from django.core.management.base import BaseCommand, CommandError
7
+ from django.conf import settings
8
+ from endoreg_db.models import VideoFile
9
+
10
+ logger = logging.getLogger(__name__)
11
+
12
+
13
+ class Command(BaseCommand):
14
+ help = 'Automated storage management and cleanup to prevent disk space issues'
15
+
16
+ def add_arguments(self, parser):
17
+ parser.add_argument(
18
+ '--dry-run',
19
+ action='store_true',
20
+ help='Show what would be cleaned without actually deleting files',
21
+ )
22
+ parser.add_argument(
23
+ '--force',
24
+ action='store_true',
25
+ help='Force cleanup even if not critically low on space',
26
+ )
27
+ parser.add_argument(
28
+ '--cleanup-frames',
29
+ action='store_true',
30
+ help='Clean up extracted video frames after processing',
31
+ )
32
+ parser.add_argument(
33
+ '--cleanup-old-videos',
34
+ action='store_true',
35
+ help='Clean up old processed videos (keep raw files)',
36
+ )
37
+ parser.add_argument(
38
+ '--cleanup-uploads',
39
+ action='store_true',
40
+ help='Clean up old upload cache files',
41
+ )
42
+ parser.add_argument(
43
+ '--cleanup-logs',
44
+ action='store_true',
45
+ help='Clean up old log files',
46
+ )
47
+ parser.add_argument(
48
+ '--max-age-days',
49
+ type=int,
50
+ default=30,
51
+ help='Maximum age in days for files to keep (default: 30)',
52
+ )
53
+ parser.add_argument(
54
+ '--emergency-threshold',
55
+ type=float,
56
+ default=95.0,
57
+ help='Storage usage percentage that triggers emergency cleanup (default: 95%%)',
58
+ )
59
+
60
+ def handle(self, *args, **options):
61
+ """Main command handler for storage management."""
62
+ self.dry_run = options['dry_run']
63
+ self.force = options['force']
64
+ self.max_age_days = options['max_age_days']
65
+ self.emergency_threshold = options['emergency_threshold']
66
+
67
+ # Validate emergency_threshold range
68
+ if not (0 <= self.emergency_threshold <= 100):
69
+ raise CommandError("The --emergency-threshold value must be between 0 and 100 (inclusive).")
70
+
71
+ if self.dry_run:
72
+ self.stdout.write(self.style.WARNING('DRY RUN MODE - No files will be deleted'))
73
+
74
+ try:
75
+ # Check current storage status
76
+ storage_info = self.get_storage_info()
77
+ self.display_storage_status(storage_info)
78
+
79
+ # Determine if emergency cleanup is needed
80
+ needs_emergency_cleanup = (
81
+ storage_info['usage_percent'] >= self.emergency_threshold
82
+ or self.force
83
+ )
84
+
85
+ if needs_emergency_cleanup:
86
+ self.stdout.write(
87
+ self.style.ERROR(
88
+ f'🚨 EMERGENCY CLEANUP TRIGGERED - Storage at {storage_info["usage_percent"]:.1f}%'
89
+ )
90
+ )
91
+ self.emergency_cleanup(options)
92
+ else:
93
+ self.stdout.write(
94
+ self.style.SUCCESS(
95
+ f'✅ Storage usage is acceptable at {storage_info["usage_percent"]:.1f}%'
96
+ )
97
+ )
98
+
99
+ # Always run maintenance cleanup if requested
100
+ if any([
101
+ options['cleanup_frames'],
102
+ options['cleanup_old_videos'],
103
+ options['cleanup_uploads'],
104
+ options['cleanup_logs']
105
+ ]):
106
+ self.maintenance_cleanup(options)
107
+
108
+ # Show final storage status
109
+ final_storage = self.get_storage_info()
110
+ self.display_cleanup_summary(storage_info, final_storage)
111
+
112
+ except Exception as e:
113
+ logger.error(f"Storage management failed: {e}")
114
+ raise CommandError(f"Storage management failed: {e}")
115
+
116
+ def get_storage_info(self):
117
+ """Get current storage information."""
118
+ try:
119
+ # Get storage stats for the root filesystem
120
+ total, used, free = shutil.disk_usage('/')
121
+ usage_percent = (used / total) * 100
122
+
123
+ # Get project-specific storage info
124
+ project_root = Path(settings.BASE_DIR).parent
125
+ project_storage = self.get_directory_size(project_root)
126
+
127
+ return {
128
+ 'total_gb': total / (1024**3),
129
+ 'used_gb': used / (1024**3),
130
+ 'free_gb': free / (1024**3),
131
+ 'usage_percent': usage_percent,
132
+ 'project_storage_gb': project_storage / (1024**3),
133
+ 'critical': usage_percent >= 95.0,
134
+ 'warning': usage_percent >= 85.0,
135
+ }
136
+ except Exception as e:
137
+ logger.error(f"Failed to get storage info: {e}")
138
+ raise
139
+
140
+ def get_directory_size(self, path):
141
+ """Calculate total size of a directory."""
142
+ total_size = 0
143
+ try:
144
+ for dirpath, dirnames, filenames in os.walk(path):
145
+ for filename in filenames:
146
+ filepath = os.path.join(dirpath, filename)
147
+ try:
148
+ total_size += os.path.getsize(filepath)
149
+ except (OSError, IOError):
150
+ continue
151
+ except Exception:
152
+ pass
153
+ return total_size
154
+
155
+ def display_storage_status(self, storage_info):
156
+ """Display current storage status."""
157
+ status_color = (
158
+ self.style.ERROR if storage_info['critical'] else
159
+ self.style.WARNING if storage_info['warning'] else
160
+ self.style.SUCCESS
161
+ )
162
+
163
+ self.stdout.write("\n" + "="*60)
164
+ self.stdout.write(status_color("💾 STORAGE STATUS"))
165
+ self.stdout.write("="*60)
166
+ self.stdout.write(f"Total Space: {storage_info['total_gb']:.1f} GB")
167
+ self.stdout.write(f"Used Space: {storage_info['used_gb']:.1f} GB")
168
+ self.stdout.write(f"Free Space: {storage_info['free_gb']:.1f} GB")
169
+ self.stdout.write(status_color(f"Usage: {storage_info['usage_percent']:.1f}%"))
170
+ self.stdout.write(f"Project Size: {storage_info['project_storage_gb']:.1f} GB")
171
+
172
+ if storage_info['critical']:
173
+ self.stdout.write(self.style.ERROR("🚨 CRITICAL: Storage critically low!"))
174
+ elif storage_info['warning']:
175
+ self.stdout.write(self.style.WARNING("⚠️ WARNING: Storage getting low"))
176
+
177
+ def emergency_cleanup(self, options):
178
+ """Perform emergency cleanup to free critical storage space."""
179
+ self.stdout.write(self.style.ERROR("\n🚨 PERFORMING EMERGENCY CLEANUP"))
180
+
181
+ total_freed = 0
182
+
183
+ # 1. AGGRESSIVE: Clean up ALL extracted frames (usually largest space saver)
184
+ frames_freed = self.cleanup_all_extracted_frames()
185
+ total_freed += frames_freed
186
+
187
+ # 2. AGGRESSIVE: Clean up ALL upload cache
188
+ uploads_freed = self.cleanup_all_uploads()
189
+ total_freed += uploads_freed
190
+
191
+ # 3. Clean up old logs
192
+ logs_freed = self.cleanup_old_logs()
193
+ total_freed += logs_freed
194
+
195
+ # 4. Clean up temporary files
196
+ temp_freed = self.cleanup_temp_files()
197
+ total_freed += temp_freed
198
+
199
+ # 5. If still critical, clean up ALL processed videos (more aggressive)
200
+ storage_info = self.get_storage_info()
201
+ if storage_info['usage_percent'] >= 90.0:
202
+ # Use 0 days to clean up ALL processed videos
203
+ videos_freed = self.cleanup_all_processed_videos()
204
+ total_freed += videos_freed
205
+
206
+ self.stdout.write(
207
+ self.style.SUCCESS(f"✅ Emergency cleanup completed: {total_freed / (1024**3):.2f} GB freed")
208
+ )
209
+
210
+ def maintenance_cleanup(self, options):
211
+ """Perform regular maintenance cleanup."""
212
+ self.stdout.write(self.style.SUCCESS("\n🔧 PERFORMING MAINTENANCE CLEANUP"))
213
+
214
+ total_freed = 0
215
+
216
+ if options['cleanup_frames']:
217
+ freed = self.cleanup_extracted_frames()
218
+ total_freed += freed
219
+
220
+ if options['cleanup_old_videos']:
221
+ freed = self.cleanup_old_processed_videos(self.max_age_days)
222
+ total_freed += freed
223
+
224
+ if options['cleanup_uploads']:
225
+ freed = self.cleanup_upload_cache()
226
+ total_freed += freed
227
+
228
+ if options['cleanup_logs']:
229
+ freed = self.cleanup_old_logs()
230
+ total_freed += freed
231
+
232
+ self.stdout.write(
233
+ self.style.SUCCESS(f"✅ Maintenance cleanup completed: {total_freed / (1024**3):.2f} GB freed")
234
+ )
235
+
236
+ def cleanup_extracted_frames(self):
237
+ """Clean up extracted video frames that are no longer needed."""
238
+ self.stdout.write("🖼️ Cleaning up extracted video frames...")
239
+
240
+ total_freed = 0
241
+ frames_dir = Path(settings.BASE_DIR).parent / 'storage' / 'frames'
242
+
243
+ if not frames_dir.exists():
244
+ return 0
245
+
246
+ # Find videos that have completed processing
247
+ completed_videos = VideoFile.objects.filter(
248
+ anonymization_tasks__status='done'
249
+ ).distinct()
250
+
251
+ for video in completed_videos:
252
+ try:
253
+ # Find frame directories for this video
254
+ video_frame_dirs = list(frames_dir.glob(f"*{video.uuid}*"))
255
+
256
+ for frame_dir in video_frame_dirs:
257
+ if frame_dir.is_dir():
258
+ dir_size = self.get_directory_size(frame_dir)
259
+
260
+ if not self.dry_run:
261
+ shutil.rmtree(frame_dir, ignore_errors=True)
262
+
263
+ total_freed += dir_size
264
+ self.stdout.write(f" Removed frames for {video.uuid}: {dir_size / (1024**2):.1f} MB")
265
+
266
+ except Exception as e:
267
+ logger.warning(f"Failed to clean frames for video {video.uuid}: {e}")
268
+ continue
269
+
270
+ self.stdout.write(f"✅ Frames cleanup: {total_freed / (1024**3):.2f} GB freed")
271
+ return total_freed
272
+
273
+ def cleanup_upload_cache(self):
274
+ """Clean up old upload cache files."""
275
+ self.stdout.write("📤 Cleaning up upload cache...")
276
+
277
+ total_freed = 0
278
+ uploads_dir = Path(settings.BASE_DIR).parent / 'storage' / 'uploads'
279
+
280
+ if not uploads_dir.exists():
281
+ return 0
282
+
283
+ cutoff_date = datetime.now() - timedelta(days=self.max_age_days)
284
+
285
+ for file_path in uploads_dir.rglob('*'):
286
+ if file_path.is_file():
287
+ try:
288
+ file_mtime = datetime.fromtimestamp(file_path.stat().st_mtime)
289
+
290
+ if file_mtime < cutoff_date:
291
+ file_size = file_path.stat().st_size
292
+
293
+ if not self.dry_run:
294
+ file_path.unlink()
295
+
296
+ total_freed += file_size
297
+
298
+ except Exception as e:
299
+ logger.warning(f"Failed to clean upload file {file_path}: {e}")
300
+ continue
301
+
302
+ self.stdout.write(f"✅ Upload cache cleanup: {total_freed / (1024**3):.2f} GB freed")
303
+ return total_freed
304
+
305
+ def cleanup_old_logs(self):
306
+ """Clean up old log files."""
307
+ self.stdout.write("📋 Cleaning up old log files...")
308
+
309
+ total_freed = 0
310
+ project_root = Path(settings.BASE_DIR).parent
311
+
312
+ # Find and clean large log files
313
+ for log_file in project_root.rglob('*.log'):
314
+ try:
315
+ if log_file.stat().st_size > 10 * 1024 * 1024: # Files larger than 10MB
316
+ file_size = log_file.stat().st_size
317
+
318
+ if not self.dry_run:
319
+ # Truncate instead of delete to preserve file handles
320
+ with open(log_file, 'w') as f:
321
+ f.write('')
322
+
323
+ total_freed += file_size
324
+ self.stdout.write(f" Truncated {log_file}: {file_size / (1024**2):.1f} MB")
325
+
326
+ except Exception as e:
327
+ logger.warning(f"Failed to clean log file {log_file}: {e}")
328
+ continue
329
+
330
+ self.stdout.write(f"✅ Log cleanup: {total_freed / (1024**3):.2f} GB freed")
331
+ return total_freed
332
+
333
+ def cleanup_temp_files(self):
334
+ """Clean up temporary files."""
335
+ self.stdout.write("🗂️ Cleaning up temporary files...")
336
+
337
+ total_freed = 0
338
+ temp_dirs = [
339
+ '/tmp',
340
+ Path(settings.BASE_DIR).parent / 'data' / 'tmp',
341
+ Path(settings.BASE_DIR).parent / 'storage' / 'tmp',
342
+ ]
343
+
344
+ for temp_dir in temp_dirs:
345
+ if not Path(temp_dir).exists():
346
+ continue
347
+
348
+ try:
349
+ for item in Path(temp_dir).glob('*'):
350
+ if item.is_file() and item.name.startswith(('tmp', 'temp')):
351
+ file_size = item.stat().st_size
352
+
353
+ if not self.dry_run:
354
+ item.unlink()
355
+
356
+ total_freed += file_size
357
+
358
+ except Exception as e:
359
+ logger.warning(f"Failed to clean temp dir {temp_dir}: {e}")
360
+ continue
361
+
362
+ self.stdout.write(f"✅ Temp files cleanup: {total_freed / (1024**3):.2f} GB freed")
363
+ return total_freed
364
+
365
+ def cleanup_old_processed_videos(self, max_age_days):
366
+ """Clean up old processed videos while keeping raw files."""
367
+ self.stdout.write(f"🎥 Cleaning up processed videos older than {max_age_days} days...")
368
+
369
+ total_freed = 0
370
+ cutoff_date = datetime.now() - timedelta(days=max_age_days)
371
+
372
+ # Find old processed videos - fix the date filtering
373
+ try:
374
+ old_videos = VideoFile.objects.filter(
375
+ created_at__lt=cutoff_date, # Use created_at instead of date_created
376
+ processed_file__isnull=False
377
+ ).exclude(
378
+ anonymization_tasks__status__in=['processing_anonymization', 'extracting_frames']
379
+ )
380
+
381
+ self.stdout.write(f"Found {old_videos.count()} processed videos older than {max_age_days} days")
382
+
383
+ except Exception as e:
384
+ # Fallback: try different date field names
385
+ try:
386
+ old_videos = VideoFile.objects.filter(
387
+ processed_file__isnull=False
388
+ ).exclude(
389
+ anonymization_tasks__status__in=['processing_anonymization', 'extracting_frames']
390
+ )
391
+ self.stdout.write(f"Using fallback filter, found {old_videos.count()} processed videos")
392
+ except Exception as e2:
393
+ logger.error(f"Failed to query videos: {e2}")
394
+ return total_freed
395
+
396
+ for video in old_videos:
397
+ try:
398
+ if video.processed_file and hasattr(video.processed_file, 'path'):
399
+ processed_path = Path(video.processed_file.path)
400
+
401
+ if processed_path.exists():
402
+ file_size = processed_path.stat().st_size
403
+
404
+ if not self.dry_run:
405
+ processed_path.unlink()
406
+ video.processed_file = None
407
+ video.save(update_fields=['processed_file'])
408
+
409
+ total_freed += file_size
410
+ self.stdout.write(f" Removed processed video {video.uuid}: {file_size / (1024**2):.1f} MB")
411
+
412
+ except Exception as e:
413
+ logger.warning(f"Failed to clean processed video {video.uuid}: {e}")
414
+ continue
415
+
416
+ self.stdout.write(f"✅ Processed videos cleanup: {total_freed / (1024**3):.2f} GB freed")
417
+ return total_freed
418
+
419
+ def cleanup_all_extracted_frames(self):
420
+ """More aggressive cleanup - remove ALL extracted frames regardless of status."""
421
+ self.stdout.write("🖼️ AGGRESSIVE: Cleaning up ALL extracted video frames...")
422
+
423
+ total_freed = 0
424
+ frames_dir = Path(settings.BASE_DIR).parent / 'storage' / 'frames'
425
+
426
+ if not frames_dir.exists():
427
+ self.stdout.write("No frames directory found")
428
+ return 0
429
+
430
+ try:
431
+ # Get directory size before cleanup
432
+ initial_size = self.get_directory_size(frames_dir)
433
+ self.stdout.write(f"Found frames directory with {initial_size / (1024**3):.2f} GB")
434
+
435
+ # Remove all frame directories and files
436
+ for item in frames_dir.iterdir():
437
+ if item.is_dir():
438
+ dir_size = self.get_directory_size(item)
439
+
440
+ if not self.dry_run:
441
+ shutil.rmtree(item, ignore_errors=True)
442
+
443
+ total_freed += dir_size
444
+ self.stdout.write(f" Removed frame directory {item.name}: {dir_size / (1024**2):.1f} MB")
445
+ elif item.is_file():
446
+ file_size = item.stat().st_size
447
+
448
+ if not self.dry_run:
449
+ item.unlink()
450
+
451
+ total_freed += file_size
452
+ self.stdout.write(f" Removed frame file {item.name}: {file_size / (1024**2):.1f} MB")
453
+
454
+ except Exception as e:
455
+ logger.error(f"Failed to clean frames directory: {e}")
456
+
457
+ self.stdout.write(f"✅ Aggressive frames cleanup: {total_freed / (1024**3):.2f} GB freed")
458
+ return total_freed
459
+
460
+ def cleanup_all_uploads(self):
461
+ """More aggressive cleanup - remove ALL upload cache files."""
462
+ self.stdout.write("📤 AGGRESSIVE: Cleaning up ALL upload cache...")
463
+
464
+ total_freed = 0
465
+ uploads_dir = Path(settings.BASE_DIR).parent / 'storage' / 'uploads'
466
+
467
+ if not uploads_dir.exists():
468
+ return 0
469
+
470
+ try:
471
+ for item in uploads_dir.rglob('*'):
472
+ if item.is_file():
473
+ file_size = item.stat().st_size
474
+
475
+ if not self.dry_run:
476
+ item.unlink()
477
+
478
+ total_freed += file_size
479
+
480
+ except Exception as e:
481
+ logger.error(f"Failed to clean uploads directory: {e}")
482
+
483
+ self.stdout.write(f"✅ Aggressive upload cleanup: {total_freed / (1024**3):.2f} GB freed")
484
+ return total_freed
485
+
486
+ def cleanup_all_processed_videos(self):
487
+ """AGGRESSIVE: Clean up ALL processed videos while keeping raw files."""
488
+ self.stdout.write("🎥 AGGRESSIVE: Cleaning up ALL processed videos...")
489
+
490
+ total_freed = 0
491
+
492
+ try:
493
+ # Find ALL processed videos
494
+ processed_videos = VideoFile.objects.filter(
495
+ processed_file__isnull=False
496
+ ).exclude(
497
+ anonymization_tasks__status__in=['processing_anonymization', 'extracting_frames']
498
+ )
499
+
500
+ self.stdout.write(f"Found {processed_videos.count()} processed videos to clean")
501
+
502
+ for video in processed_videos:
503
+ try:
504
+ freed = self._cleanup_processed_video_file(video)
505
+ total_freed += freed
506
+ except Exception as e:
507
+ logger.warning(f"Failed to clean processed video {video.uuid}: {e}")
508
+ continue
509
+
510
+ except Exception as e:
511
+ logger.error(f"Failed to query processed videos: {e}")
512
+
513
+ self.stdout.write(f"✅ Aggressive processed videos cleanup: {total_freed / (1024**3):.2f} GB freed")
514
+ return total_freed
515
+
516
+ def _cleanup_processed_video_file(self, video):
517
+ """
518
+ Helper to clean up a single processed video file, update DB, and return freed size in bytes.
519
+ """
520
+ if video.processed_file and hasattr(video.processed_file, 'path'):
521
+ processed_path = Path(video.processed_file.path)
522
+ if processed_path.exists():
523
+ file_size = processed_path.stat().st_size
524
+ if not self.dry_run:
525
+ processed_path.unlink()
526
+ video.processed_file = None
527
+ video.save(update_fields=['processed_file'])
528
+ self.stdout.write(f" Removed processed video {video.uuid}: {file_size / (1024**2):.1f} MB")
529
+ return file_size
530
+ return 0
531
+
532
+ def display_cleanup_summary(self, before, after):
533
+ """Display cleanup summary."""
534
+ freed_gb = before['used_gb'] - after['used_gb']
535
+
536
+ self.stdout.write("\n" + "="*60)
537
+ self.stdout.write(self.style.SUCCESS("📊 CLEANUP SUMMARY"))
538
+ self.stdout.write("="*60)
539
+ self.stdout.write(f"Before: {before['used_gb']:.1f} GB used ({before['usage_percent']:.1f}%)")
540
+ self.stdout.write(f"After: {after['used_gb']:.1f} GB used ({after['usage_percent']:.1f}%)")
541
+ self.stdout.write(self.style.SUCCESS(f"Freed: {freed_gb:.2f} GB"))
542
+
543
+ if after['usage_percent'] < 90.0:
544
+ self.stdout.write(self.style.SUCCESS("✅ Storage levels are now healthy!"))
545
+ elif after['usage_percent'] < 95.0:
546
+ self.stdout.write(self.style.WARNING("⚠️ Storage levels improved but still high"))
547
+ else:
548
+ self.stdout.write(self.style.ERROR("🚨 Storage levels still critical - manual intervention needed"))