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

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  1. endoreg_db/admin.py +26 -26
  2. endoreg_db/api_urls.py +4 -0
  3. endoreg_db/apps.py +12 -0
  4. endoreg_db/assets/dummy_model.ckpt +1 -0
  5. endoreg_db/codemods/readme.md +88 -0
  6. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  7. endoreg_db/config/env.py +101 -0
  8. endoreg_db/data/__init__.py +12 -0
  9. endoreg_db/data/ai_model/data.yaml +1 -1
  10. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  11. endoreg_db/data/ai_model_label/label-set/data.yaml +20 -1
  12. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  13. endoreg_db/data/center/data.yaml +13 -12
  14. endoreg_db/data/center_shift/ukw.yaml +9 -0
  15. endoreg_db/data/db_summary.csv +58 -0
  16. endoreg_db/data/db_summary.xlsx +0 -0
  17. endoreg_db/data/disease/misc.yaml +1 -2
  18. endoreg_db/data/endoscopy_processor/data.yaml +3 -0
  19. endoreg_db/data/event/cardiology.yaml +0 -13
  20. endoreg_db/data/examination/examinations/data.yaml +14 -9
  21. endoreg_db/data/examination_indication/endoscopy.yaml +30 -30
  22. endoreg_db/data/examination_indication_classification/endoscopy.yaml +11 -11
  23. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  24. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  25. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  26. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  27. endoreg_db/data/finding/complication.yaml +16 -0
  28. endoreg_db/data/finding/data.yaml +3 -46
  29. endoreg_db/data/finding/examination_setting.yaml +16 -0
  30. endoreg_db/data/finding/medication_related.yaml +18 -0
  31. endoreg_db/data/finding/outcome.yaml +12 -0
  32. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  33. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  34. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  35. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  36. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  37. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  38. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  39. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  40. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  41. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  42. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  43. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  44. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  45. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  46. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  47. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  48. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  49. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  50. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  51. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  52. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_circularity_default.yaml +0 -2
  53. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  54. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  55. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  56. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_nice.yaml +4 -7
  57. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_paris.yaml +0 -8
  58. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_planarity_default.yaml +6 -13
  59. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  60. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_surface_intact_default.yaml +3 -6
  61. endoreg_db/data/{finding_location_classification_choice/colonoscopy.yaml → finding_classification_choice/colonoscopy_location.yaml} +11 -22
  62. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  63. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  64. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  65. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  66. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  67. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  68. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  69. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  70. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  71. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  72. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +8 -3
  73. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +6 -6
  74. endoreg_db/data/finding_type/data.yaml +23 -10
  75. endoreg_db/data/gender/data.yaml +8 -1
  76. endoreg_db/data/information_source/annotation.yaml +6 -0
  77. endoreg_db/data/information_source/prediction.yaml +7 -0
  78. endoreg_db/data/information_source_type/data.yaml +8 -0
  79. endoreg_db/data/lab_value/misc.yaml +43 -0
  80. endoreg_db/data/medication/anticoagulation.yaml +5 -5
  81. endoreg_db/data/medication/tah.yaml +5 -5
  82. endoreg_db/data/medication_intake_time/base.yaml +4 -4
  83. endoreg_db/data/names_first/first_names.yaml +3 -0
  84. endoreg_db/data/pdf_type/data.yaml +26 -2
  85. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  86. endoreg_db/data/qualification/m2.yaml +39 -0
  87. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  88. endoreg_db/data/qualification/sonography.yaml +36 -0
  89. endoreg_db/data/qualification_type/base.yaml +29 -0
  90. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  91. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +5 -0
  92. endoreg_db/data/requirement/age.yaml +26 -0
  93. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  94. endoreg_db/data/requirement/disease_cardiovascular.yaml +6 -6
  95. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +9 -6
  96. endoreg_db/data/requirement/disease_hepatology.yaml +1 -1
  97. endoreg_db/data/requirement/disease_misc.yaml +3 -3
  98. endoreg_db/data/requirement/disease_renal.yaml +18 -2
  99. endoreg_db/data/requirement/{colonoscopy_indications.yaml → endoscopy_bleeding_risk.yaml} +6 -3
  100. endoreg_db/data/requirement/event_cardiology.yaml +17 -17
  101. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  102. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  103. endoreg_db/data/requirement/gender.yaml +25 -0
  104. endoreg_db/data/requirement/lab_value.yaml +352 -31
  105. endoreg_db/data/requirement/medication.yaml +93 -0
  106. endoreg_db/data/requirement_operator/age.yaml +13 -0
  107. endoreg_db/data/requirement_operator/lab_operators.yaml +36 -35
  108. endoreg_db/data/requirement_operator/model_operators.yaml +13 -7
  109. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  110. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  111. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +42 -2
  112. endoreg_db/data/requirement_type/requirement_types.yaml +82 -0
  113. endoreg_db/data/shift/endoscopy.yaml +21 -0
  114. endoreg_db/data/shift_type/base.yaml +35 -0
  115. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  116. endoreg_db/data/unit/concentration.yaml +23 -0
  117. endoreg_db/exceptions.py +19 -0
  118. endoreg_db/forms/patient_finding_intervention_form.py +4 -5
  119. endoreg_db/forms/patient_form.py +7 -6
  120. endoreg_db/forms/questionnaires/__init__.py +1 -1
  121. endoreg_db/forms/questionnaires/tto_questionnaire.py +19 -19
  122. endoreg_db/helpers/count_db.py +45 -0
  123. endoreg_db/helpers/data_loader.py +208 -0
  124. endoreg_db/helpers/default_objects.py +359 -0
  125. endoreg_db/helpers/interact.py +6 -0
  126. endoreg_db/helpers/test_video_helper.py +119 -0
  127. endoreg_db/logger_conf.py +140 -0
  128. endoreg_db/management/__init__.py +1 -0
  129. endoreg_db/management/commands/__init__.py +1 -0
  130. endoreg_db/management/commands/anonymize_video.py +0 -0
  131. endoreg_db/management/commands/check_auth.py +125 -0
  132. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  133. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  134. endoreg_db/management/commands/fix_video_paths.py +165 -0
  135. endoreg_db/management/commands/import_fallback_video.py +203 -0
  136. endoreg_db/management/commands/import_report.py +298 -0
  137. endoreg_db/management/commands/import_video.py +422 -0
  138. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  139. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  140. endoreg_db/management/commands/load_ai_model_data.py +2 -7
  141. endoreg_db/management/commands/load_base_db_data.py +1 -0
  142. endoreg_db/management/commands/load_endoscope_data.py +2 -2
  143. endoreg_db/management/commands/load_examination_indication_data.py +2 -3
  144. endoreg_db/management/commands/load_finding_data.py +49 -92
  145. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +0 -1
  146. endoreg_db/management/commands/load_information_source.py +13 -7
  147. endoreg_db/management/commands/load_name_data.py +37 -0
  148. endoreg_db/management/commands/load_qualification_data.py +59 -0
  149. endoreg_db/management/commands/load_requirement_data.py +30 -6
  150. endoreg_db/management/commands/load_shift_data.py +60 -0
  151. endoreg_db/management/commands/load_tag_data.py +57 -0
  152. endoreg_db/management/commands/register_ai_model.py +1 -1
  153. endoreg_db/management/commands/start_filewatcher.py +106 -0
  154. endoreg_db/management/commands/storage_management.py +548 -0
  155. endoreg_db/management/commands/summarize_db_content.py +189 -0
  156. endoreg_db/management/commands/validate_video.py +204 -0
  157. endoreg_db/management/commands/validate_video_files.py +161 -0
  158. endoreg_db/management/commands/video_validation.py +22 -0
  159. endoreg_db/migrations/0001_initial.py +625 -813
  160. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  161. endoreg_db/models/__init__.py +270 -307
  162. endoreg_db/models/administration/__init__.py +116 -0
  163. endoreg_db/models/{ai_model → administration/ai}/__init__.py +6 -1
  164. endoreg_db/models/administration/ai/active_model.py +35 -0
  165. endoreg_db/models/administration/ai/ai_model.py +156 -0
  166. endoreg_db/models/{ai_model → administration/ai}/model_type.py +6 -1
  167. endoreg_db/models/administration/case/__init__.py +19 -0
  168. endoreg_db/models/administration/case/case.py +114 -0
  169. endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +3 -3
  170. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +3 -10
  171. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +2 -4
  172. endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +1 -3
  173. endoreg_db/models/{center → administration/center}/__init__.py +3 -1
  174. endoreg_db/models/administration/center/center.py +61 -0
  175. endoreg_db/models/administration/center/center_product.py +64 -0
  176. endoreg_db/models/{center → administration/center}/center_resource.py +19 -3
  177. endoreg_db/models/administration/center/center_shift.py +88 -0
  178. endoreg_db/models/administration/center/center_waste.py +30 -0
  179. endoreg_db/models/administration/permissions/__init__.py +44 -0
  180. endoreg_db/models/administration/person/__init__.py +24 -0
  181. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  182. endoreg_db/models/administration/person/employee/employee.py +35 -0
  183. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  184. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  185. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  186. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  187. endoreg_db/models/administration/person/names/__init__.py +0 -0
  188. endoreg_db/models/{persons → administration/person/names}/first_name.py +1 -1
  189. endoreg_db/models/{persons → administration/person/names}/last_name.py +2 -3
  190. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  191. endoreg_db/models/administration/person/patient/patient.py +460 -0
  192. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  193. endoreg_db/models/administration/person/user/__init__.py +5 -0
  194. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  195. endoreg_db/models/administration/product/product.py +97 -0
  196. endoreg_db/models/administration/product/product_group.py +39 -0
  197. endoreg_db/models/administration/product/product_material.py +54 -0
  198. endoreg_db/models/{product → administration/product}/product_weight.py +9 -0
  199. endoreg_db/models/{product → administration/product}/reference_product.py +26 -11
  200. endoreg_db/models/administration/qualification/__init__.py +7 -0
  201. endoreg_db/models/administration/qualification/qualification.py +37 -0
  202. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  203. endoreg_db/models/administration/shift/__init__.py +9 -0
  204. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  205. endoreg_db/models/administration/shift/shift.py +51 -0
  206. endoreg_db/models/administration/shift/shift_type.py +108 -0
  207. endoreg_db/models/label/__init__.py +24 -1
  208. endoreg_db/models/label/annotation/__init__.py +12 -0
  209. endoreg_db/models/label/annotation/image_classification.py +84 -0
  210. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  211. endoreg_db/models/label/label.py +45 -74
  212. endoreg_db/models/label/label_set.py +53 -0
  213. endoreg_db/models/label/label_type.py +29 -0
  214. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  215. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  216. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  217. endoreg_db/models/label/video_segmentation_label.py +31 -0
  218. endoreg_db/models/{annotation → label}/video_segmentation_labelset.py +7 -0
  219. endoreg_db/models/media/__init__.py +14 -0
  220. endoreg_db/models/media/frame/__init__.py +3 -0
  221. endoreg_db/models/media/frame/frame.py +111 -0
  222. endoreg_db/models/media/pdf/__init__.py +11 -0
  223. endoreg_db/models/media/pdf/raw_pdf.py +608 -0
  224. endoreg_db/models/media/pdf/report_file.py +162 -0
  225. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  226. endoreg_db/models/media/video/__init__.py +4 -0
  227. endoreg_db/models/media/video/create_from_file.py +336 -0
  228. endoreg_db/models/media/video/pipe_1.py +195 -0
  229. endoreg_db/models/media/video/pipe_2.py +105 -0
  230. endoreg_db/models/media/video/refactor_plan.md +0 -0
  231. endoreg_db/models/media/video/video_file.py +680 -0
  232. endoreg_db/models/media/video/video_file_ai.py +443 -0
  233. endoreg_db/models/media/video/video_file_anonymize.py +348 -0
  234. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  235. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  236. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  237. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  238. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  239. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  240. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  241. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  242. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  243. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  244. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  245. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  246. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +129 -0
  247. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  248. endoreg_db/models/media/video/video_file_frames.py +0 -0
  249. endoreg_db/models/media/video/video_file_io.py +166 -0
  250. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  251. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  252. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  253. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  254. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  255. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  256. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  257. endoreg_db/models/media/video/video_file_meta.py +11 -0
  258. endoreg_db/models/media/video/video_file_segments.py +209 -0
  259. endoreg_db/models/medical/__init__.py +146 -0
  260. endoreg_db/models/{contraindication → medical/contraindication}/__init__.py +1 -5
  261. endoreg_db/models/{disease.py → medical/disease.py} +60 -52
  262. endoreg_db/models/{event.py → medical/event.py} +31 -54
  263. endoreg_db/models/{examination → medical/examination}/__init__.py +1 -1
  264. endoreg_db/models/medical/examination/examination.py +148 -0
  265. endoreg_db/models/{examination → medical/examination}/examination_indication.py +64 -35
  266. endoreg_db/models/{examination → medical/examination}/examination_time.py +0 -4
  267. endoreg_db/models/{examination → medical/examination}/examination_time_type.py +1 -8
  268. endoreg_db/models/{examination → medical/examination}/examination_type.py +1 -7
  269. endoreg_db/models/medical/finding/__init__.py +18 -0
  270. endoreg_db/models/medical/finding/finding.py +96 -0
  271. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  272. endoreg_db/models/{finding → medical/finding}/finding_intervention.py +2 -10
  273. endoreg_db/models/medical/finding/finding_type.py +35 -0
  274. endoreg_db/models/medical/hardware/__init__.py +8 -0
  275. endoreg_db/models/{hardware → medical/hardware}/endoscope.py +28 -23
  276. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  277. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  278. endoreg_db/models/{medication → medical/medication}/medication.py +1 -3
  279. endoreg_db/models/{medication → medical/medication}/medication_indication_type.py +8 -3
  280. endoreg_db/models/{medication → medical/medication}/medication_intake_time.py +21 -3
  281. endoreg_db/models/{medication → medical/medication}/medication_schedule.py +13 -5
  282. endoreg_db/models/{organ → medical/organ}/__init__.py +3 -6
  283. endoreg_db/models/medical/patient/__init__.py +56 -0
  284. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  285. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  286. endoreg_db/models/medical/patient/patient_event.py +75 -0
  287. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  288. endoreg_db/models/{persons → medical}/patient/patient_examination_indication.py +21 -9
  289. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  290. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  291. endoreg_db/models/{patient → medical/patient}/patient_finding_intervention.py +15 -1
  292. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  293. endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +40 -15
  294. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  295. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  296. endoreg_db/models/{risk → medical/risk}/risk_type.py +0 -4
  297. endoreg_db/models/{data_file/metadata → metadata}/__init__.py +6 -0
  298. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  299. endoreg_db/models/metadata/model_meta.py +193 -0
  300. endoreg_db/models/metadata/model_meta_logic.py +236 -0
  301. endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +28 -13
  302. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  303. endoreg_db/models/metadata/sensitive_meta_logic.py +643 -0
  304. endoreg_db/models/metadata/video_meta.py +332 -0
  305. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  306. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  307. endoreg_db/models/other/__init__.py +17 -0
  308. endoreg_db/models/other/distribution/date_value_distribution.py +0 -2
  309. endoreg_db/models/other/distribution/numeric_value_distribution.py +30 -2
  310. endoreg_db/models/{emission → other/emission}/emission_factor.py +15 -6
  311. endoreg_db/models/{persons → other}/gender.py +8 -3
  312. endoreg_db/models/other/information_source.py +159 -0
  313. endoreg_db/models/other/material.py +10 -2
  314. endoreg_db/models/other/resource.py +6 -2
  315. endoreg_db/models/other/tag.py +27 -0
  316. endoreg_db/models/other/transport_route.py +13 -2
  317. endoreg_db/models/{unit.py → other/unit.py} +16 -6
  318. endoreg_db/models/other/waste.py +10 -3
  319. endoreg_db/models/requirement/requirement.py +556 -114
  320. endoreg_db/models/requirement/requirement_evaluation/__init__.py +4 -132
  321. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  322. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  323. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +80 -87
  324. endoreg_db/models/requirement/requirement_operator.py +132 -14
  325. endoreg_db/models/requirement/requirement_set.py +181 -21
  326. endoreg_db/models/rule/__init__.py +13 -0
  327. endoreg_db/models/{rules → rule}/rule.py +6 -3
  328. endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +0 -2
  329. endoreg_db/models/{rules → rule}/rule_type.py +0 -2
  330. endoreg_db/models/{rules → rule}/ruleset.py +0 -2
  331. endoreg_db/models/state/__init__.py +12 -0
  332. endoreg_db/models/state/abstract.py +11 -0
  333. endoreg_db/models/state/audit_ledger.py +150 -0
  334. endoreg_db/models/state/label_video_segment.py +22 -0
  335. endoreg_db/models/state/raw_pdf.py +187 -0
  336. endoreg_db/models/state/sensitive_meta.py +46 -0
  337. endoreg_db/models/state/video.py +232 -0
  338. endoreg_db/models/upload_job.py +99 -0
  339. endoreg_db/models/utils.py +135 -0
  340. endoreg_db/models/video_metadata.py +66 -0
  341. endoreg_db/models/video_processing.py +153 -0
  342. endoreg_db/renames.yml +8 -0
  343. endoreg_db/root_urls.py +9 -0
  344. endoreg_db/schemas/__init__.py +0 -0
  345. endoreg_db/schemas/examination_evaluation.py +27 -0
  346. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  347. endoreg_db/serializers/__init__.py +147 -10
  348. endoreg_db/serializers/{raw_pdf_meta_validation.py → _old/raw_pdf_meta_validation.py} +3 -3
  349. endoreg_db/serializers/{raw_video_meta_validation.py → _old/raw_video_meta_validation.py} +18 -14
  350. endoreg_db/serializers/_old/video.py +71 -0
  351. endoreg_db/serializers/administration/__init__.py +14 -0
  352. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  353. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  354. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  355. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  356. endoreg_db/serializers/administration/center.py +9 -0
  357. endoreg_db/serializers/administration/gender.py +9 -0
  358. endoreg_db/serializers/anonymization.py +66 -0
  359. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  360. endoreg_db/serializers/examination/__init__.py +10 -0
  361. endoreg_db/serializers/examination/base.py +46 -0
  362. endoreg_db/serializers/examination/dropdown.py +21 -0
  363. endoreg_db/serializers/examination_serializer.py +12 -0
  364. endoreg_db/serializers/finding/__init__.py +5 -0
  365. endoreg_db/serializers/finding/finding.py +54 -0
  366. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  367. endoreg_db/serializers/finding_classification/choice.py +19 -0
  368. endoreg_db/serializers/finding_classification/classification.py +13 -0
  369. endoreg_db/serializers/label/__init__.py +7 -0
  370. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  371. endoreg_db/serializers/label/label.py +15 -0
  372. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  373. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  374. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  375. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  376. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  377. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  378. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  379. endoreg_db/serializers/meta/__init__.py +19 -0
  380. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  381. endoreg_db/serializers/meta/report_meta.py +53 -0
  382. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  383. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  384. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  385. endoreg_db/serializers/meta/video_meta.py +39 -0
  386. endoreg_db/serializers/misc/__init__.py +14 -0
  387. endoreg_db/serializers/misc/file_overview.py +152 -0
  388. endoreg_db/serializers/misc/stats.py +33 -0
  389. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  390. endoreg_db/serializers/misc/upload_job.py +71 -0
  391. endoreg_db/serializers/misc/vop_patient_data.py +120 -0
  392. endoreg_db/serializers/patient/__init__.py +11 -0
  393. endoreg_db/serializers/patient/patient.py +86 -0
  394. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  395. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  396. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  397. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  398. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  399. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  400. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  401. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  402. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  403. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  404. endoreg_db/serializers/pdf/__init__.py +5 -0
  405. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  406. endoreg_db/serializers/report/__init__.py +9 -0
  407. endoreg_db/serializers/report/mixins.py +45 -0
  408. endoreg_db/serializers/report/report.py +105 -0
  409. endoreg_db/serializers/report/report_list.py +22 -0
  410. endoreg_db/serializers/report/secure_file_url.py +26 -0
  411. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  412. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  413. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  414. endoreg_db/serializers/video/__init__.py +7 -0
  415. endoreg_db/serializers/video/segmentation.py +263 -0
  416. endoreg_db/serializers/video/video_file_brief.py +10 -0
  417. endoreg_db/serializers/video/video_file_detail.py +83 -0
  418. endoreg_db/serializers/video/video_file_list.py +67 -0
  419. endoreg_db/serializers/video/video_metadata.py +105 -0
  420. endoreg_db/serializers/video/video_processing_history.py +153 -0
  421. endoreg_db/services/__init__.py +5 -0
  422. endoreg_db/services/anonymization.py +223 -0
  423. endoreg_db/services/examination_evaluation.py +149 -0
  424. endoreg_db/services/finding_description_service.py +0 -0
  425. endoreg_db/services/lookup_service.py +241 -0
  426. endoreg_db/services/lookup_store.py +122 -0
  427. endoreg_db/services/ollama_api_docs.py +1528 -0
  428. endoreg_db/services/pdf_import.py +993 -0
  429. endoreg_db/services/polling_coordinator.py +288 -0
  430. endoreg_db/services/pseudonym_service.py +89 -0
  431. endoreg_db/services/requirements_object.py +147 -0
  432. endoreg_db/services/segment_sync.py +155 -0
  433. endoreg_db/services/storage_aware_video_processor.py +344 -0
  434. endoreg_db/services/video_import.py +915 -0
  435. endoreg_db/tasks/upload_tasks.py +207 -0
  436. endoreg_db/tasks/video_ingest.py +157 -0
  437. endoreg_db/tasks/video_processing_tasks.py +327 -0
  438. endoreg_db/urls/__init__.py +72 -0
  439. endoreg_db/urls/anonymization.py +32 -0
  440. endoreg_db/urls/auth.py +16 -0
  441. endoreg_db/urls/classification.py +39 -0
  442. endoreg_db/urls/examination.py +54 -0
  443. endoreg_db/urls/files.py +6 -0
  444. endoreg_db/urls/label_video_segment_validate.py +33 -0
  445. endoreg_db/urls/label_video_segments.py +44 -0
  446. endoreg_db/urls/media.py +32 -0
  447. endoreg_db/urls/patient.py +19 -0
  448. endoreg_db/urls/pdf.py +0 -0
  449. endoreg_db/urls/report.py +78 -0
  450. endoreg_db/urls/requirements.py +13 -0
  451. endoreg_db/urls/sensitive_meta.py +36 -0
  452. endoreg_db/urls/stats.py +46 -0
  453. endoreg_db/urls/upload.py +20 -0
  454. endoreg_db/urls/video.py +119 -0
  455. endoreg_db/urls.py +6 -283
  456. endoreg_db/utils/__init__.py +66 -57
  457. endoreg_db/utils/ai/__init__.py +9 -0
  458. endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +1 -4
  459. endoreg_db/{models/ai_model/lightning → utils/ai}/inference_dataset.py +0 -1
  460. endoreg_db/{models/ai_model/lightning → utils/ai}/multilabel_classification_net.py +14 -10
  461. endoreg_db/{models/ai_model/lightning → utils/ai}/postprocess.py +15 -5
  462. endoreg_db/utils/ai/predict.py +291 -0
  463. endoreg_db/{models/ai_model/lightning → utils/ai}/preprocess.py +1 -1
  464. endoreg_db/utils/calc_duration_seconds.py +24 -0
  465. endoreg_db/utils/case_generator/__init__.py +0 -0
  466. endoreg_db/utils/check_video_files.py +148 -0
  467. endoreg_db/utils/dataloader.py +50 -12
  468. endoreg_db/utils/dates.py +21 -0
  469. endoreg_db/utils/env.py +33 -0
  470. endoreg_db/utils/extract_specific_frames.py +72 -0
  471. endoreg_db/utils/file_operations.py +29 -1
  472. endoreg_db/utils/fix_video_path_direct.py +141 -0
  473. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  474. endoreg_db/utils/links/__init__.py +0 -0
  475. endoreg_db/utils/links/requirement_link.py +193 -0
  476. endoreg_db/utils/mime_types.py +0 -0
  477. endoreg_db/utils/names.py +2 -0
  478. endoreg_db/utils/paths.py +100 -82
  479. endoreg_db/utils/permissions.py +143 -0
  480. endoreg_db/utils/pipelines/Readme.md +235 -0
  481. endoreg_db/utils/pipelines/__init__.py +0 -0
  482. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  483. endoreg_db/utils/product/__init__.py +0 -0
  484. endoreg_db/utils/product/sum_emissions.py +20 -0
  485. endoreg_db/utils/product/sum_weights.py +18 -0
  486. endoreg_db/utils/pydantic_models/db_config.py +1 -1
  487. endoreg_db/utils/requirement_helpers.py +0 -0
  488. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  489. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  490. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  491. endoreg_db/utils/translation.py +27 -0
  492. endoreg_db/utils/validate_video_detailed.py +357 -0
  493. endoreg_db/utils/video/__init__.py +19 -6
  494. endoreg_db/utils/video/extract_frames.py +37 -70
  495. endoreg_db/utils/video/ffmpeg_wrapper.py +772 -0
  496. endoreg_db/utils/video/names.py +42 -0
  497. endoreg_db/utils/video/streaming_processor.py +312 -0
  498. endoreg_db/utils/video/video_splitter.py +94 -0
  499. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  500. endoreg_db/views/__init__.py +282 -2
  501. endoreg_db/views/anonymization/__init__.py +27 -0
  502. endoreg_db/views/anonymization/media_management.py +454 -0
  503. endoreg_db/views/anonymization/overview.py +216 -0
  504. endoreg_db/views/anonymization/validate.py +63 -0
  505. endoreg_db/views/auth/__init__.py +13 -0
  506. endoreg_db/views/{views.py → auth/keycloak.py} +19 -13
  507. endoreg_db/views/examination/__init__.py +33 -0
  508. endoreg_db/views/examination/examination.py +37 -0
  509. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  510. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  511. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  512. endoreg_db/views/examination/get_findings.py +41 -0
  513. endoreg_db/views/examination/get_instruments.py +18 -0
  514. endoreg_db/views/examination/get_interventions.py +14 -0
  515. endoreg_db/views/finding/__init__.py +9 -0
  516. endoreg_db/views/finding/finding.py +112 -0
  517. endoreg_db/views/finding/get_classifications.py +14 -0
  518. endoreg_db/views/finding/get_interventions.py +17 -0
  519. endoreg_db/views/finding_classification/__init__.py +13 -0
  520. endoreg_db/views/finding_classification/base.py +0 -0
  521. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  522. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  523. endoreg_db/views/label/__init__.py +5 -0
  524. endoreg_db/views/label/label.py +15 -0
  525. endoreg_db/views/label_video_segment/__init__.py +16 -0
  526. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  527. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  528. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  529. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  530. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  531. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  532. endoreg_db/views/label_video_segment/validate.py +226 -0
  533. endoreg_db/views/media/__init__.py +9 -0
  534. endoreg_db/views/media/pdf_media.py +386 -0
  535. endoreg_db/views/media/video_media.py +272 -0
  536. endoreg_db/views/meta/__init__.py +15 -0
  537. endoreg_db/views/meta/available_files_list.py +146 -0
  538. endoreg_db/views/meta/report_meta.py +53 -0
  539. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  540. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  541. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  542. endoreg_db/views/misc/__init__.py +63 -0
  543. endoreg_db/views/misc/center.py +13 -0
  544. endoreg_db/views/misc/gender.py +14 -0
  545. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  546. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  547. endoreg_db/views/misc/secure_url_validate.py +79 -0
  548. endoreg_db/views/misc/stats.py +220 -0
  549. endoreg_db/views/misc/translation.py +182 -0
  550. endoreg_db/views/misc/upload_views.py +240 -0
  551. endoreg_db/views/patient/__init__.py +5 -0
  552. endoreg_db/views/patient/patient.py +210 -0
  553. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  554. endoreg_db/views/patient_examination/__init__.py +11 -0
  555. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  556. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  557. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  558. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  559. endoreg_db/views/patient_examination/video.py +194 -0
  560. endoreg_db/views/patient_finding/__init__.py +7 -0
  561. endoreg_db/views/patient_finding/base.py +0 -0
  562. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  563. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  564. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  565. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  566. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  567. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  568. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  569. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  570. endoreg_db/views/pdf/__init__.py +11 -0
  571. endoreg_db/views/pdf/pdf_media.py +239 -0
  572. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  573. endoreg_db/views/pdf/reimport.py +151 -0
  574. endoreg_db/views/report/__init__.py +9 -0
  575. endoreg_db/views/report/report_list.py +112 -0
  576. endoreg_db/views/report/report_with_secure_url.py +28 -0
  577. endoreg_db/views/report/start_examination.py +7 -0
  578. endoreg_db/views/requirement/__init__.py +10 -0
  579. endoreg_db/views/requirement/evaluate.py +279 -0
  580. endoreg_db/views/requirement/lookup.py +483 -0
  581. endoreg_db/views/requirement/lookup_store.py +252 -0
  582. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  583. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  584. endoreg_db/views/stats/__init__.py +13 -0
  585. endoreg_db/views/stats/stats_views.py +229 -0
  586. endoreg_db/views/video/__init__.py +72 -0
  587. endoreg_db/views/video/correction.py +672 -0
  588. endoreg_db/views/video/media/__init__.py +23 -0
  589. endoreg_db/views/video/media/task_status.py +49 -0
  590. endoreg_db/views/video/media/video_analyze.py +52 -0
  591. endoreg_db/views/video/media/video_apply_mask.py +48 -0
  592. endoreg_db/views/video/media/video_correction.py +21 -0
  593. endoreg_db/views/video/media/video_download_processed.py +58 -0
  594. endoreg_db/views/video/media/video_media.py +158 -0
  595. endoreg_db/views/video/media/video_meta.py +29 -0
  596. endoreg_db/views/video/media/video_processing_history.py +24 -0
  597. endoreg_db/views/video/media/video_remove_frames.py +48 -0
  598. endoreg_db/views/video/media/video_reprocess.py +40 -0
  599. endoreg_db/views/video/reimport.py +192 -0
  600. endoreg_db/views/video/segmentation.py +274 -0
  601. endoreg_db/views/{views_for_timeline.py → video/timeline.py} +3 -3
  602. endoreg_db/views/video/video_examination_viewset.py +329 -0
  603. endoreg_db/views/video/video_stream.py +188 -0
  604. endoreg_db-0.8.1.dist-info/METADATA +384 -0
  605. endoreg_db-0.8.1.dist-info/RECORD +789 -0
  606. endoreg_db/data/agl_service/data.yaml +0 -19
  607. endoreg_db/data/finding_location_classification/colonoscopy.yaml +0 -46
  608. endoreg_db/data/finding_morphology_classification/colonoscopy.yaml +0 -48
  609. endoreg_db/data/finding_morphology_classification_choice/colonoscopy_size.yaml +0 -57
  610. endoreg_db/management/commands/_load_model_template.py +0 -41
  611. endoreg_db/management/commands/delete_all.py +0 -18
  612. endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
  613. endoreg_db/management/commands/fix_auth_permission.py +0 -20
  614. endoreg_db/management/commands/load_active_model_data.py +0 -45
  615. endoreg_db/management/commands/load_g_play_data.py +0 -113
  616. endoreg_db/management/commands/load_logging_data.py +0 -39
  617. endoreg_db/management/commands/load_lx_data.py +0 -64
  618. endoreg_db/management/commands/load_medication_indication_data.py +0 -63
  619. endoreg_db/management/commands/load_medication_indication_type_data.py +0 -41
  620. endoreg_db/management/commands/load_medication_intake_time_data.py +0 -41
  621. endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
  622. endoreg_db/management/commands/load_network_data.py +0 -57
  623. endoreg_db/migrations/0002_alter_frame_image_alter_rawframe_image.py +0 -23
  624. endoreg_db/migrations/0003_alter_frame_image_alter_rawframe_image.py +0 -23
  625. endoreg_db/migrations/0004_alter_rawvideofile_file_alter_video_file.py +0 -25
  626. endoreg_db/migrations/0005_rawvideofile_frame_count_and_more.py +0 -33
  627. endoreg_db/migrations/0006_frame_extracted_rawframe_extracted.py +0 -23
  628. endoreg_db/migrations/0007_rename_pseudo_patient_video_patient_and_more.py +0 -24
  629. endoreg_db/migrations/0008_remove_reportfile_patient_examination_and_more.py +0 -48
  630. endoreg_db/migrations/0009_requirementoperator_requirementsettype_and_more.py +0 -154
  631. endoreg_db/models/ai_model/active_model.py +0 -9
  632. endoreg_db/models/ai_model/ai_model.py +0 -90
  633. endoreg_db/models/ai_model/lightning/__init__.py +0 -3
  634. endoreg_db/models/ai_model/lightning/predict.py +0 -172
  635. endoreg_db/models/ai_model/lightning/prediction_visualizer.py +0 -55
  636. endoreg_db/models/ai_model/lightning/run_visualizer.py +0 -21
  637. endoreg_db/models/ai_model/model_meta.py +0 -240
  638. endoreg_db/models/annotation/__init__.py +0 -32
  639. endoreg_db/models/annotation/anonymized_image_annotation.py +0 -115
  640. endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -117
  641. endoreg_db/models/annotation/image_classification.py +0 -86
  642. endoreg_db/models/annotation/video_segmentation_annotation.py +0 -52
  643. endoreg_db/models/case/__init__.py +0 -1
  644. endoreg_db/models/case/case.py +0 -34
  645. endoreg_db/models/center/center.py +0 -51
  646. endoreg_db/models/center/center_product.py +0 -33
  647. endoreg_db/models/center/center_waste.py +0 -16
  648. endoreg_db/models/data_file/__init__.py +0 -39
  649. endoreg_db/models/data_file/base_classes/__init__.py +0 -7
  650. endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -98
  651. endoreg_db/models/data_file/base_classes/abstract_pdf.py +0 -127
  652. endoreg_db/models/data_file/base_classes/abstract_video.py +0 -806
  653. endoreg_db/models/data_file/base_classes/frame_helpers.py +0 -17
  654. endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +0 -19
  655. endoreg_db/models/data_file/base_classes/utils.py +0 -58
  656. endoreg_db/models/data_file/frame.py +0 -29
  657. endoreg_db/models/data_file/import_classes/__init__.py +0 -18
  658. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
  659. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
  660. endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
  661. endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -254
  662. endoreg_db/models/data_file/import_classes/raw_video.py +0 -290
  663. endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -290
  664. endoreg_db/models/data_file/metadata/video_meta.py +0 -199
  665. endoreg_db/models/data_file/report_file.py +0 -56
  666. endoreg_db/models/data_file/video/__init__.py +0 -11
  667. endoreg_db/models/data_file/video/import_meta.py +0 -25
  668. endoreg_db/models/data_file/video/video.py +0 -196
  669. endoreg_db/models/data_file/video_segment.py +0 -214
  670. endoreg_db/models/examination/examination.py +0 -67
  671. endoreg_db/models/finding/__init__.py +0 -11
  672. endoreg_db/models/finding/finding.py +0 -75
  673. endoreg_db/models/finding/finding_location_classification.py +0 -94
  674. endoreg_db/models/finding/finding_morphology_classification.py +0 -89
  675. endoreg_db/models/finding/finding_type.py +0 -22
  676. endoreg_db/models/hardware/__init__.py +0 -2
  677. endoreg_db/models/information_source.py +0 -65
  678. endoreg_db/models/laboratory/__init__.py +0 -1
  679. endoreg_db/models/laboratory/lab_value.py +0 -162
  680. endoreg_db/models/logging/__init__.py +0 -11
  681. endoreg_db/models/logging/agl_service.py +0 -19
  682. endoreg_db/models/logging/base.py +0 -22
  683. endoreg_db/models/logging/log_type.py +0 -23
  684. endoreg_db/models/logging/network_device.py +0 -27
  685. endoreg_db/models/lx/__init__.py +0 -4
  686. endoreg_db/models/lx/client.py +0 -57
  687. endoreg_db/models/lx/identity.py +0 -34
  688. endoreg_db/models/lx/permission.py +0 -18
  689. endoreg_db/models/lx/user.py +0 -16
  690. endoreg_db/models/network/__init__.py +0 -9
  691. endoreg_db/models/network/agl_service.py +0 -38
  692. endoreg_db/models/network/network_device.py +0 -58
  693. endoreg_db/models/network/network_device_type.py +0 -23
  694. endoreg_db/models/other/distribution.py +0 -5
  695. endoreg_db/models/patient/__init__.py +0 -24
  696. endoreg_db/models/patient/patient_examination.py +0 -182
  697. endoreg_db/models/patient/patient_finding.py +0 -143
  698. endoreg_db/models/patient/patient_finding_location.py +0 -120
  699. endoreg_db/models/patient/patient_finding_morphology.py +0 -166
  700. endoreg_db/models/permissions/__init__.py +0 -44
  701. endoreg_db/models/persons/__init__.py +0 -34
  702. endoreg_db/models/persons/examiner/__init__.py +0 -2
  703. endoreg_db/models/persons/examiner/examiner.py +0 -60
  704. endoreg_db/models/persons/examiner/examiner_type.py +0 -2
  705. endoreg_db/models/persons/patient/__init__.py +0 -8
  706. endoreg_db/models/persons/patient/patient.py +0 -389
  707. endoreg_db/models/persons/patient/patient_disease.py +0 -22
  708. endoreg_db/models/persons/patient/patient_event.py +0 -52
  709. endoreg_db/models/persons/patient/patient_lab_sample.py +0 -108
  710. endoreg_db/models/persons/patient/patient_medication.py +0 -59
  711. endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -88
  712. endoreg_db/models/persons/portal_user_information.py +0 -27
  713. endoreg_db/models/prediction/__init__.py +0 -8
  714. endoreg_db/models/prediction/image_classification.py +0 -51
  715. endoreg_db/models/prediction/video_prediction_meta.py +0 -306
  716. endoreg_db/models/product/product.py +0 -110
  717. endoreg_db/models/product/product_group.py +0 -27
  718. endoreg_db/models/product/product_material.py +0 -28
  719. endoreg_db/models/questionnaires/__init__.py +0 -114
  720. endoreg_db/models/quiz/__init__.py +0 -9
  721. endoreg_db/models/quiz/quiz_answer.py +0 -41
  722. endoreg_db/models/quiz/quiz_question.py +0 -54
  723. endoreg_db/models/report_reader/report_reader_config.py +0 -53
  724. endoreg_db/models/rules/__init__.py +0 -5
  725. endoreg_db/queries/get/__init__.py +0 -6
  726. endoreg_db/queries/get/center.py +0 -42
  727. endoreg_db/queries/get/model.py +0 -13
  728. endoreg_db/queries/get/patient.py +0 -14
  729. endoreg_db/queries/get/patient_examination.py +0 -20
  730. endoreg_db/queries/get/report_file.py +0 -33
  731. endoreg_db/queries/get/video.py +0 -31
  732. endoreg_db/serializers/ai_model.py +0 -19
  733. endoreg_db/serializers/annotation.py +0 -14
  734. endoreg_db/serializers/center.py +0 -11
  735. endoreg_db/serializers/examination.py +0 -33
  736. endoreg_db/serializers/frame.py +0 -9
  737. endoreg_db/serializers/hardware.py +0 -21
  738. endoreg_db/serializers/label.py +0 -22
  739. endoreg_db/serializers/patient.py +0 -33
  740. endoreg_db/serializers/prediction.py +0 -10
  741. endoreg_db/serializers/raw_pdf_anony_text_validation.py +0 -137
  742. endoreg_db/serializers/report_file.py +0 -7
  743. endoreg_db/serializers/video.py +0 -20
  744. endoreg_db/serializers/video_segmentation.py +0 -574
  745. endoreg_db/tests.py +0 -3
  746. endoreg_db/utils/legacy_ocr.py +0 -201
  747. endoreg_db/utils/video/transcode_videofile.py +0 -111
  748. endoreg_db/views/patient_views.py +0 -90
  749. endoreg_db/views/raw_pdf_anony_text_validation_views.py +0 -95
  750. endoreg_db/views/raw_pdf_meta_validation_views.py +0 -111
  751. endoreg_db/views/raw_video_meta_validation_views.py +0 -148
  752. endoreg_db/views/report_views.py +0 -96
  753. endoreg_db/views/video_segmentation_views.py +0 -166
  754. endoreg_db-0.6.4.dist-info/METADATA +0 -161
  755. endoreg_db-0.6.4.dist-info/RECORD +0 -470
  756. /endoreg_db/{case_generator/__init__.py → api/serializers/finding_descriptions.py} +0 -0
  757. /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
  758. /endoreg_db/{queries/get/prediction.py → data/shift/m2.yaml} +0 -0
  759. /endoreg_db/{queries/get/video_import_meta.py → factories/__init__.py} +0 -0
  760. /endoreg_db/{queries/get/video_prediction_meta.py → helpers/__init__.py} +0 -0
  761. /endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +0 -0
  762. /endoreg_db/models/{persons → administration/person}/person.py +0 -0
  763. /endoreg_db/models/{product → administration/product}/__init__.py +0 -0
  764. /endoreg_db/models/{report_reader → media/pdf/report_reader}/__init__.py +0 -0
  765. /endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +0 -0
  766. /endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +0 -0
  767. /endoreg_db/models/{medication → medical/medication}/__init__.py +0 -0
  768. /endoreg_db/models/{medication → medical/medication}/medication_indication.py +0 -0
  769. /endoreg_db/models/{risk → medical/risk}/__init__.py +0 -0
  770. /endoreg_db/models/{risk → medical/risk}/risk.py +0 -0
  771. /endoreg_db/models/{emission → other/emission}/__init__.py +0 -0
  772. /endoreg_db/models/{rules → rule}/rule_applicator.py +0 -0
  773. /endoreg_db/{case_generator → utils/case_generator}/case_generator.py +0 -0
  774. /endoreg_db/{case_generator → utils/case_generator}/lab_sample_factory.py +0 -0
  775. /endoreg_db/{case_generator → utils/case_generator}/utils.py +0 -0
  776. /endoreg_db/views/{csrf.py → misc/csrf.py} +0 -0
  777. {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.1.dist-info}/WHEEL +0 -0
  778. {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.1.dist-info}/licenses/LICENSE +0 -0
@@ -1,63 +1,45 @@
1
1
  from django.core.management.base import BaseCommand
2
2
  from endoreg_db.models import (
3
3
  Finding, FindingType, Examination,
4
- FindingLocationClassification, FindingLocationClassificationChoice,
4
+ FindingClassification, FindingClassificationType, FindingClassificationChoice,
5
5
  Organ,
6
- FindingMorphologyClassificationType, FindingMorphologyClassification,
7
- FindingMorphologyClassificationChoice,
8
6
  FindingIntervention, FindingInterventionType, LabValue, Contraindication
9
7
 
10
8
  )
11
9
  from ...utils import load_model_data_from_yaml
12
10
  from ...data import (
13
11
  FINDING_DATA_DIR, FINDING_TYPE_DATA_DIR,
14
- FINDING_LOCATION_CLASSIFICATION_DATA_DIR,
15
- FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR,
16
- FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR,
17
- FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR,
18
- FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR,
19
12
  FINDING_INTERVETION_DATA_DIR,
20
- FINIDNG_INTERVENTION_TYPE_DATA_DIR
13
+ FINIDNG_INTERVENTION_TYPE_DATA_DIR,
14
+ FINDING_CLASSIFICATION_TYPE_DATA_DIR,
15
+ FINDING_CLASSIFICATION_DATA_DIR,
16
+ FINDING_CLASSIFICATION_CHOICE_DATA_DIR
21
17
  )
22
18
 
23
- MODEL_0 = FindingType
24
- MODEL_1 = Finding
25
- MODEL_2 = FindingLocationClassificationChoice
26
- MODEL_3 = FindingLocationClassification
27
- MODEL_4 = FindingMorphologyClassificationType
28
- MODEL_5 = FindingMorphologyClassification
29
- MODEL_6 = FindingMorphologyClassificationChoice
30
- MODEL_7 = FindingInterventionType
31
- MODEL_8 = FindingIntervention
32
-
33
19
  IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
34
- MODEL_7.__name__,
35
- MODEL_8.__name__,
36
- MODEL_0.__name__,
37
- MODEL_1.__name__,
38
- MODEL_2.__name__,
39
- MODEL_3.__name__,
40
- MODEL_4.__name__,
41
- MODEL_5.__name__,
42
- MODEL_6.__name__,
20
+ FindingInterventionType.__name__,
21
+ FindingIntervention.__name__,
22
+ FindingType.__name__,
23
+ Finding.__name__,
24
+ FindingClassificationType.__name__,
25
+ FindingClassificationChoice.__name__,
26
+ FindingClassification.__name__,
43
27
  ]
44
28
 
45
29
  IMPORT_METADATA = {
46
- MODEL_0.__name__: {
30
+ FindingType.__name__: {
47
31
  "dir": FINDING_TYPE_DATA_DIR, # e.g. "interventions"
48
- "model": MODEL_0, # e.g. Intervention
32
+ "model": FindingType, # e.g. Intervention
49
33
  "foreign_keys": [], # e.g. ["intervention_types"]
50
34
  "foreign_key_models": [] # e.g. [InterventionType]
51
35
  },
52
36
  Finding.__name__: {
53
37
  "dir": FINDING_DATA_DIR, # e.g. "interventions"
54
- "model": MODEL_1, # e.g. Intervention
38
+ "model": Finding, # e.g. Intervention
55
39
  "foreign_keys": [
56
40
  "finding_types",
57
41
  "examinations",
58
42
  "finding_interventions",
59
- "causing_finding_interventions",
60
- "opt_causing_finding_interventions",
61
43
  ], # e.g. ["intervention_types"]
62
44
  "foreign_key_models": [
63
45
  FindingType,
@@ -67,65 +49,6 @@ IMPORT_METADATA = {
67
49
  FindingIntervention,
68
50
  ] # e.g. [InterventionType]
69
51
  },
70
- MODEL_2.__name__: {
71
- "dir": FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
72
- "model": MODEL_2, # e.g. Intervention
73
- "foreign_keys": [
74
- "organs"
75
- ], # e.g. ["intervention_types"]
76
- "foreign_key_models": [
77
- Organ
78
- ] # e.g. [InterventionType]
79
- },
80
- MODEL_3.__name__: {
81
- "dir": FINDING_LOCATION_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
82
- "model": MODEL_3, # e.g. Intervention
83
- "foreign_keys": [
84
- "examinations",
85
- "finding_types",
86
- "findings",
87
- "choices"
88
- ], # e.g. ["intervention_types"]
89
- "foreign_key_models": [
90
- Examination,
91
- FindingType,
92
- Finding,
93
- FindingLocationClassificationChoice
94
- ] # e.g. [InterventionType]
95
- },
96
- MODEL_4.__name__: {
97
- "dir": FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR, # e.g. "interventions"
98
- "model": MODEL_4, # e.g. Intervention
99
- "foreign_keys": [
100
- "required_by_findings",
101
- "optional_for_findings"
102
- ], # e.g. ["intervention_types"]
103
- "foreign_key_models": [
104
- Finding,
105
- Finding
106
- ] # e.g. [InterventionType]
107
- },
108
-
109
- MODEL_5.__name__: {
110
- "dir": FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
111
- "model": MODEL_5, # e.g. Intervention
112
- "foreign_keys": [
113
- "classification_type",
114
- ],
115
- "foreign_key_models": [
116
- FindingMorphologyClassificationType,
117
- ]
118
- },
119
- MODEL_6.__name__: {
120
- "dir": FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
121
- "model": MODEL_6, # e.g. Intervention
122
- "foreign_keys": [
123
- "classification",
124
- ],
125
- "foreign_key_models": [
126
- FindingMorphologyClassification,
127
- ]
128
- },
129
52
  FindingInterventionType.__name__: {
130
53
  "dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR, # e.g. "interventions"
131
54
  "model": FindingInterventionType, # e.g. Intervention
@@ -146,6 +69,40 @@ IMPORT_METADATA = {
146
69
  Contraindication
147
70
  ] # e.g. [InterventionType]
148
71
  },
72
+ FindingClassificationType.__name__: {
73
+ "dir": FINDING_CLASSIFICATION_TYPE_DATA_DIR, # e.g. "interventions"
74
+ "model": FindingClassificationType, # e.g. Intervention
75
+ "foreign_keys": [], # e.g. ["intervention_types"]
76
+ "foreign_key_models": [] # e.g. [InterventionType]
77
+ },
78
+ FindingClassification.__name__: {
79
+ "dir": FINDING_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
80
+ "model": FindingClassification, # e.g. Intervention
81
+ "foreign_keys": [
82
+ "classification_types",
83
+ "findings",
84
+ "examinations",
85
+ "finding_types",
86
+ "choices"
87
+ ], # e.g. ["intervention_types"]
88
+ "foreign_key_models": [
89
+ FindingClassificationType,
90
+ Finding,
91
+ Examination,
92
+ FindingType,
93
+ FindingClassificationChoice,
94
+ ] # e.g. [InterventionType]
95
+ },
96
+ FindingClassificationChoice.__name__: {
97
+ "dir": FINDING_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
98
+ "model": FindingClassificationChoice, # e.g. Intervention
99
+ "foreign_keys": [
100
+ # "classifications",
101
+ ], # e.g. ["intervention_types"]
102
+ "foreign_key_models": [
103
+ # FindingClassification
104
+ ] # e.g. [InterventionType]
105
+ },
149
106
  }
150
107
 
151
108
  class Command(BaseCommand):
@@ -7,7 +7,6 @@ from endoreg_db.models import (
7
7
  Product,
8
8
  ProductGroup,
9
9
  ReferenceProduct,
10
- ProductGroup,
11
10
  TransportRoute,
12
11
  CenterWaste,
13
12
  CenterResource,
@@ -1,24 +1,30 @@
1
1
  from django.conf import settings
2
2
  import os
3
3
  from django.core.management.base import BaseCommand
4
- from ...models import InformationSource
4
+ from ...models import InformationSource, InformationSourceType
5
5
  from ...utils import load_model_data_from_yaml
6
- from ...data import INFORMATION_DATA_DIR
6
+ from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
7
7
 
8
8
  SOURCE_DIR = INFORMATION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
9
9
 
10
- MODEL_0 = InformationSource
11
10
 
12
11
  IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
13
- MODEL_0.__name__,
12
+ InformationSourceType.__name__,
13
+ InformationSource.__name__,
14
14
  ]
15
15
 
16
16
  IMPORT_METADATA = {
17
- MODEL_0.__name__: {
18
- "dir": SOURCE_DIR, # e.g. "interventions"
19
- "model": MODEL_0, # e.g. Intervention
17
+ InformationSourceType.__name__: {
18
+ "dir": INFORMATION_SOURCE_TYPE_DATA_DIR, # e.g. "intervention_type"
19
+ "model": InformationSourceType, # e.g. InterventionType
20
20
  "foreign_keys": [], # e.g. ["intervention_types"]
21
21
  "foreign_key_models": [] # e.g. [InterventionType]
22
+ },
23
+ InformationSource.__name__: {
24
+ "dir": SOURCE_DIR, # e.g. "interventions"
25
+ "model": InformationSource, # e.g. Intervention
26
+ "foreign_keys": ["information_source_types"], # e.g. ["intervention_types"]
27
+ "foreign_key_models": [InformationSourceType] # e.g. [InterventionType]
22
28
  }
23
29
  }
24
30
 
@@ -0,0 +1,37 @@
1
+ # endoreg_db/management/commands/generate_names.py
2
+
3
+ import os
4
+ from django.core.management.base import BaseCommand
5
+ from endoreg_db.utils import collect_center_names # Import your function here
6
+ from pathlib import Path
7
+
8
+ class Command(BaseCommand):
9
+ help = "Generate first_names.yaml and last_names.yaml from center data"
10
+
11
+ def add_arguments(self, parser):
12
+ # Adding an argument for the input file path
13
+ # parser.add_argument(
14
+ # '--input_file_path',
15
+ # type=str,
16
+ # required=False,
17
+ # help="Path to the input YAML file containing center data",
18
+ # default="data/center/data.yaml",
19
+ # )
20
+ # parser.add_argument(
21
+ # '--output-dir',
22
+ # type=str,
23
+ # default=os.getcwd(),
24
+ # help="Directory where the output files will be saved (default: current directory)",
25
+ # )
26
+ pass
27
+
28
+ def handle(self, *args, **options):
29
+
30
+ # Run the function with the provided arguments
31
+ try:
32
+ collect_center_names()
33
+ self.stdout.write(self.style.SUCCESS("Successfully generated YAML files."))
34
+ except Exception as e:
35
+ self.stderr.write(self.style.ERROR(f"An error occurred: {e}"))
36
+
37
+ self.stderr.write(self.style.ERROR(f"PWD: {os.getcwd()}"))
@@ -0,0 +1,59 @@
1
+ from django.core.management.base import BaseCommand
2
+ from ...models import Qualification, QualificationType
3
+ from ...utils import load_model_data_from_yaml
4
+ from ...data import QUALIFICATION_DATA_DIR
5
+
6
+ SOURCE_DIR = QUALIFICATION_DATA_DIR # qualification data directory
7
+
8
+ model_0 = QualificationType
9
+ model_1 = Qualification
10
+
11
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
+ model_0.__name__,
13
+ model_1.__name__,
14
+ ]
15
+
16
+ IMPORT_METADATA = {
17
+ model_0.__name__: {
18
+ "dir": SOURCE_DIR, # e.g. "interventions"
19
+ "model": model_0, # e.g. Intervention
20
+ "foreign_keys": [], # e.g. ["intervention_types"]
21
+ "foreign_key_models": [] # e.g. [InterventionType]
22
+ },
23
+ model_1.__name__: {
24
+ "dir": SOURCE_DIR, # e.g. "interventions"
25
+ "model": model_1, # e.g. Intervention
26
+ "foreign_keys": ["qualification_types"], # e.g. ["intervention_types"]
27
+ "foreign_key_models": [model_0] # e.g. [InterventionType]
28
+ }
29
+ }
30
+
31
+ class Command(BaseCommand):
32
+ help = """Load all .yaml files in the data/qualification directory
33
+ into the Qualification / Qualification Type model"""
34
+
35
+ def add_arguments(self, parser):
36
+ """
37
+ Adds the --verbose flag to the command-line parser to enable detailed output.
38
+ """
39
+ parser.add_argument(
40
+ '--verbose',
41
+ action='store_true',
42
+ help='Display verbose output',
43
+ )
44
+
45
+ def handle(self, *args, **options):
46
+ """
47
+ Loads data from YAML files into the QualificationType and Qualification models.
48
+
49
+ Iterates over predefined models and imports their data from YAML files using associated metadata. Supports verbose output if enabled via command-line options.
50
+ """
51
+ verbose = options['verbose']
52
+ for model_name in IMPORT_MODELS:
53
+ _metadata = IMPORT_METADATA[model_name]
54
+ load_model_data_from_yaml(
55
+ self,
56
+ model_name,
57
+ _metadata,
58
+ verbose
59
+ )
@@ -12,8 +12,8 @@ from endoreg_db.models import (
12
12
  Event,
13
13
  LabValue,
14
14
  Finding,
15
- FindingMorphologyClassificationChoice,
16
- FindingLocationClassificationChoice,
15
+ FindingClassification,
16
+ FindingClassificationChoice,
17
17
  FindingIntervention,
18
18
  InformationSource,
19
19
  Unit,
@@ -22,7 +22,12 @@ from endoreg_db.models import (
22
22
  MedicationIndication,
23
23
  MedicationIndicationType,
24
24
  MedicationSchedule,
25
+ Medication, # Added Medication model
26
+ MedicationIntakeTime,
27
+ Tag,
28
+ ExaminationRequirementSet, # Added to avoid circular import issues
25
29
  )
30
+ from endoreg_db.models.other.gender import Gender
26
31
  from ...utils import load_model_data_from_yaml
27
32
  from ...data import (
28
33
  REQUIREMENT_TYPE_DATA_DIR,
@@ -30,6 +35,7 @@ from ...data import (
30
35
  REQUIREMENT_DATA_DIR,
31
36
  REQUIREMENT_SET_TYPE_DATA_DIR,
32
37
  REQUIREMENT_SET_DATA_DIR,
38
+ EXAMINATION_REQUIREMENT_SET_DATA_DIR
33
39
  )
34
40
 
35
41
 
@@ -38,6 +44,7 @@ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
38
44
  RequirementOperator.__name__,
39
45
  Requirement.__name__,
40
46
  RequirementSetType.__name__,
47
+ ExaminationRequirementSet.__name__,
41
48
  RequirementSet.__name__,
42
49
  ]
43
50
 
@@ -54,6 +61,13 @@ IMPORT_METADATA = {
54
61
  "foreign_keys": [], # e.g. ["intervention_types"]
55
62
  "foreign_key_models": [], # e.g. [InterventionType]
56
63
  },
64
+ ExaminationRequirementSet.__name__: {
65
+ "dir": EXAMINATION_REQUIREMENT_SET_DATA_DIR, # e.g. "interventions"
66
+ "model": ExaminationRequirementSet, # e.g. Intervention
67
+ "foreign_keys": ["examinations",], # Through model uses foreign keys of both models
68
+ "foreign_key_models": [Examination,],
69
+ },
70
+ # ExaminationRequirementSet.__name__,
57
71
  Requirement.__name__: {
58
72
  "dir": REQUIREMENT_DATA_DIR, # e.g. "interventions"
59
73
  "model": Requirement, # e.g. Intervention
@@ -68,14 +82,17 @@ IMPORT_METADATA = {
68
82
  "events",
69
83
  "lab_values",
70
84
  "findings",
71
- "finding_morphology_classification_choices",
72
- "finding_location_classification_choices",
85
+ "finding_classifications",
86
+ "finding_classification_choices", # updated from finding_morphology_classification_choices
73
87
  "finding_interventions",
74
88
  "risks",
75
89
  "risk_types",
76
90
  "medication_indications",
77
91
  "medication_indication_types",
78
92
  "medication_schedules",
93
+ "medications", # Added medications
94
+ "medication_intake_times",
95
+ "genders"
79
96
  ],
80
97
  "foreign_key_models": [
81
98
  RequirementType,
@@ -88,14 +105,17 @@ IMPORT_METADATA = {
88
105
  Event,
89
106
  LabValue,
90
107
  Finding,
91
- FindingMorphologyClassificationChoice,
92
- FindingLocationClassificationChoice,
108
+ FindingClassification,
109
+ FindingClassificationChoice,
93
110
  FindingIntervention,
94
111
  Risk,
95
112
  RiskType,
96
113
  MedicationIndication,
97
114
  MedicationIndicationType,
98
115
  MedicationSchedule,
116
+ Medication, # Added Medication model
117
+ MedicationIntakeTime,
118
+ Gender
99
119
  ],
100
120
  },
101
121
  RequirementSetType.__name__: {
@@ -112,12 +132,16 @@ IMPORT_METADATA = {
112
132
  "requirements", # This is a many-to-many field
113
133
  "links_to_sets",
114
134
  "information_sources",
135
+ "tags",
136
+ "reqset_exam_links"
115
137
  ], # e.g. ["intervention_types"]
116
138
  "foreign_key_models": [
117
139
  RequirementSetType,
118
140
  Requirement,
119
141
  RequirementSet,
120
142
  InformationSource,
143
+ Tag,
144
+ ExaminationRequirementSet
121
145
  ], # e.g. [InterventionType]
122
146
  },
123
147
  }
@@ -0,0 +1,60 @@
1
+ from django.core.management.base import BaseCommand
2
+ from ...models import Shift, ShiftType
3
+ from ...utils import load_model_data_from_yaml
4
+ from ...data import REPORT_READER_FLAG_DATA_DIR
5
+
6
+ SOURCE_DIR = REPORT_READER_FLAG_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
7
+
8
+ model_0 = ShiftType
9
+ model_1 = Shift
10
+
11
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
+ model_0.__name__,
13
+ ]
14
+
15
+ IMPORT_METADATA = {
16
+ model_0.__name__: {
17
+ "dir": SOURCE_DIR, # e.g. "interventions"
18
+ "model": model_0, # e.g. Intervention
19
+ "foreign_keys": [], # e.g. ["intervention_types"]
20
+ "foreign_key_models": [] # e.g. [InterventionType]
21
+ },
22
+ model_1.__name__: {
23
+ "dir": SOURCE_DIR, # e.g. "interventions"
24
+ "model": model_1, # e.g. Intervention
25
+ "foreign_keys": ["shift_types"], # e.g. ["intervention_types"]
26
+ "foreign_key_models": [model_0] # e.g. [InterventionType]
27
+ }
28
+ }
29
+
30
+ class Command(BaseCommand):
31
+ help = """Load all .yaml files in the data/shift directory
32
+ into the Shift and ShiftType model"""
33
+
34
+ def add_arguments(self, parser):
35
+ """
36
+ Adds the --verbose command-line option to enable detailed output during execution.
37
+ """
38
+ parser.add_argument(
39
+ '--verbose',
40
+ action='store_true',
41
+ help='Display verbose output',
42
+ )
43
+
44
+ def handle(self, *args, **options):
45
+ """
46
+ Loads YAML data files into models defined in IMPORT_MODELS using provided metadata.
47
+
48
+ Iterates over each model specified in IMPORT_MODELS, retrieves its import metadata,
49
+ and calls the data loading utility to populate the database from YAML files. Supports
50
+ optional verbose output if enabled via command-line options.
51
+ """
52
+ verbose = options['verbose']
53
+ for model_name in IMPORT_MODELS:
54
+ _metadata = IMPORT_METADATA[model_name]
55
+ load_model_data_from_yaml(
56
+ self,
57
+ model_name,
58
+ _metadata,
59
+ verbose
60
+ )
@@ -0,0 +1,57 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import (
3
+ Tag,
4
+
5
+ )
6
+
7
+ from ...utils import load_model_data_from_yaml
8
+ from ...data import (
9
+ TAG_DATA_DIR
10
+ )
11
+
12
+
13
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
14
+ Tag.__name__,
15
+ ]
16
+
17
+ IMPORT_METADATA = {
18
+ Tag.__name__: {
19
+ "dir": TAG_DATA_DIR, # e.g. "interventions"
20
+ "model": Tag, # e.g. Intervention
21
+ "foreign_keys": [], # e.g. ["intervention_types"]
22
+ "foreign_key_models": [], # e.g. [InterventionType]
23
+ },
24
+ }
25
+
26
+
27
+ class Command(BaseCommand):
28
+ help = """Load all requirement-related YAML files from their respective directories
29
+ into the database, including RequirementType, RequirementOperator, Requirement,
30
+ RequirementSetType, and RequirementSet models"""
31
+
32
+ def add_arguments(self, parser):
33
+ """
34
+ Add command-line arguments to enable verbose output.
35
+
36
+ Adds an optional '--verbose' flag to the command parser. When specified,
37
+ this flag causes the command to display detailed output during execution.
38
+ """
39
+ parser.add_argument(
40
+ "--verbose",
41
+ action="store_true",
42
+ help="Display verbose output",
43
+ )
44
+
45
+ def handle(self, *args, **options):
46
+ """
47
+ Executes data import for requirement models from YAML files.
48
+
49
+ Retrieves the verbosity setting from the command options and iterates over each model
50
+ listed in IMPORT_MODELS. For each model, it obtains the corresponding metadata from
51
+ IMPORT_METADATA and calls a helper to load the YAML data into the database. Verbose mode
52
+ enables detailed output during the process.
53
+ """
54
+ verbose = options["verbose"]
55
+ for model_name in IMPORT_MODELS:
56
+ _metadata = IMPORT_METADATA[model_name]
57
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -25,7 +25,7 @@ class Command(BaseCommand):
25
25
  parser.add_argument('model_meta_path', type=str)
26
26
 
27
27
  def handle(self, *args, **options):
28
- model_meta_path = Path(options['model_meta_path']).resolve()
28
+ model_meta_path = Path(options['model_meta_path'])
29
29
 
30
30
  with open(model_meta_path, 'r') as f:
31
31
  model_meta = json.load(f)
@@ -0,0 +1,106 @@
1
+ """
2
+ Django Management Command for File Watcher Service
3
+
4
+ This command provides Django integration for the file watcher service.
5
+ """
6
+
7
+ from django.core.management.base import BaseCommand
8
+ from django.conf import settings
9
+ import sys
10
+ import os
11
+ from pathlib import Path
12
+
13
+
14
+ class Command(BaseCommand):
15
+ help = """
16
+ Start the file watcher service for automatic video and PDF processing.
17
+
18
+ This command monitors:
19
+ - data/raw_videos/ for video files (.mp4, .avi, .mov, .mkv, .webm, .m4v)
20
+ - data/raw_pdfs/ for PDF files (.pdf)
21
+
22
+ When files are detected, they are automatically processed with:
23
+ - Video: Import, anonymization, and segmentation
24
+ - PDF: Import and anonymization
25
+ """
26
+
27
+ def add_arguments(self, parser):
28
+ parser.add_argument(
29
+ '--test',
30
+ action='store_true',
31
+ help='Test the file watcher configuration without starting monitoring',
32
+ )
33
+ parser.add_argument(
34
+ '--existing',
35
+ action='store_true',
36
+ help='Process existing files in the directories before starting monitoring',
37
+ )
38
+ parser.add_argument(
39
+ '--log-level',
40
+ choices=['DEBUG', 'INFO', 'WARNING', 'ERROR'],
41
+ default='INFO',
42
+ help='Set logging level (default: INFO)',
43
+ )
44
+
45
+ def handle(self, *args, **options):
46
+ self.stdout.write(self.style.SUCCESS("Starting File Watcher Service"))
47
+
48
+ # Set environment variables
49
+ os.environ['WATCHER_LOG_LEVEL'] = options['log_level']
50
+
51
+ try:
52
+ # Add project root to path
53
+ project_root = Path(settings.BASE_DIR)
54
+ if str(project_root) not in sys.path:
55
+ sys.path.insert(0, str(project_root))
56
+
57
+ # Import the file watcher service from the correct location
58
+ file_watcher_path = project_root / 'scripts' / 'file_watcher.py'
59
+
60
+ if not file_watcher_path.exists():
61
+ self.stdout.write(self.style.ERROR(f"❌ File watcher script not found: {file_watcher_path}"))
62
+ return
63
+
64
+ # Import the module dynamically
65
+ import importlib.util
66
+ spec = importlib.util.spec_from_file_location("file_watcher", file_watcher_path)
67
+ file_watcher_module = importlib.util.module_from_spec(spec)
68
+ spec.loader.exec_module(file_watcher_module)
69
+
70
+ FileWatcherService = file_watcher_module.FileWatcherService
71
+
72
+ if options['test']:
73
+ self.stdout.write("Testing file watcher configuration...")
74
+ service = FileWatcherService()
75
+ try:
76
+ service._validate_django_setup()
77
+ except Exception as e:
78
+ self.stdout.write(self.style.ERROR(f"❌ Validation failed: {e}"))
79
+ return
80
+ self.stdout.write(self.style.SUCCESS("✅ File watcher test passed"))
81
+ return
82
+
83
+ # Create and start the service
84
+ service = FileWatcherService()
85
+
86
+ if options['existing']:
87
+ self.stdout.write("Processing existing files...")
88
+ service._process_existing_files()
89
+ self.stdout.write(self.style.SUCCESS("✅ Existing files processed"))
90
+ return
91
+
92
+ self.stdout.write("Starting file monitoring...")
93
+ self.stdout.write(f"Video directory: {service.video_dir}")
94
+ self.stdout.write(f"PDF directory: {service.pdf_dir}")
95
+ self.stdout.write("Press Ctrl+C to stop")
96
+
97
+ service.start()
98
+
99
+ except KeyboardInterrupt:
100
+ self.stdout.write(self.style.WARNING("\n⚠️ File watcher stopped by user"))
101
+ except Exception as e:
102
+ self.stdout.write(self.style.ERROR(f"❌ Error: {str(e)}"))
103
+ if options['verbosity'] >= 2:
104
+ import traceback
105
+ self.stdout.write(traceback.format_exc())
106
+ sys.exit(1)