endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.9.2__py3-none-any.whl

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

Potentially problematic release.


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

Files changed (402) hide show
  1. endoreg_db/data/__init__.py +22 -8
  2. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +0 -1
  3. endoreg_db/data/examination/examinations/data.yaml +114 -14
  4. endoreg_db/data/examination/time-type/data.yaml +0 -3
  5. endoreg_db/data/examination_indication/endoscopy.yaml +108 -173
  6. endoreg_db/data/examination_indication_classification/endoscopy.yaml +0 -70
  7. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +33 -37
  8. endoreg_db/data/finding/00_generic.yaml +35 -0
  9. endoreg_db/data/finding/00_generic_complication.yaml +9 -0
  10. endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
  11. endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
  12. endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
  13. endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
  14. endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
  15. endoreg_db/data/finding_classification/00_generic.yaml +44 -0
  16. endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
  17. endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
  18. endoreg_db/data/finding_classification/{colonoscopy_bowel_preparation.yaml → 02_colonoscopy_baseline.yaml} +35 -20
  19. endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
  20. endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
  21. endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
  22. endoreg_db/data/finding_classification_choice/{yes_no_na.yaml → 00_generic.yaml} +5 -1
  23. endoreg_db/data/finding_classification_choice/{examination_setting_generic_types.yaml → 00_generic_baseline.yaml} +10 -2
  24. endoreg_db/data/finding_classification_choice/{complication_generic_types.yaml → 00_generic_complication.yaml} +1 -1
  25. endoreg_db/data/finding_classification_choice/{histology.yaml → 00_generic_histology.yaml} +1 -4
  26. endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
  27. endoreg_db/data/finding_classification_choice/{bowel_preparation.yaml → 02_colonoscopy_bowel_preparation.yaml} +1 -30
  28. endoreg_db/data/{_examples/finding_classification_choice/colonoscopy_not_complete_reason.yaml → finding_classification_choice/02_colonoscopy_generic.yaml} +1 -1
  29. endoreg_db/data/finding_classification_choice/{histology_polyp.yaml → 02_colonoscopy_histology.yaml} +1 -1
  30. endoreg_db/data/{_examples/finding_classification_choice/colonoscopy_location.yaml → finding_classification_choice/02_colonoscopy_location.yaml} +23 -4
  31. endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
  32. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
  33. endoreg_db/data/{_examples/finding_classification_choice/colon_lesion_paris.yaml → finding_classification_choice/02_colonoscopy_polyp_morphology.yaml} +26 -8
  34. endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
  35. endoreg_db/data/finding_classification_type/{colonoscopy_basic.yaml → 00_generic.yaml} +18 -13
  36. endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
  37. endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
  38. endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
  39. endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
  40. endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
  41. endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
  42. endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
  43. endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
  44. endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
  45. endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
  46. endoreg_db/data/finding_type/data.yaml +8 -12
  47. endoreg_db/data/requirement/01_patient_data.yaml +93 -0
  48. endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
  49. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +0 -2
  50. endoreg_db/data/requirement_set/90_coloreg.yaml +20 -8
  51. endoreg_db/exceptions.py +0 -1
  52. endoreg_db/forms/examination_form.py +1 -1
  53. endoreg_db/helpers/data_loader.py +124 -52
  54. endoreg_db/helpers/default_objects.py +116 -81
  55. endoreg_db/import_files/__init__.py +27 -0
  56. endoreg_db/import_files/context/__init__.py +7 -0
  57. endoreg_db/import_files/context/default_sensitive_meta.py +81 -0
  58. endoreg_db/import_files/context/ensure_center.py +17 -0
  59. endoreg_db/import_files/context/file_lock.py +66 -0
  60. endoreg_db/import_files/context/import_context.py +43 -0
  61. endoreg_db/import_files/context/validate_directories.py +56 -0
  62. endoreg_db/import_files/file_storage/__init__.py +15 -0
  63. endoreg_db/import_files/file_storage/create_report_file.py +76 -0
  64. endoreg_db/import_files/file_storage/create_video_file.py +75 -0
  65. endoreg_db/import_files/file_storage/sensitive_meta_storage.py +39 -0
  66. endoreg_db/import_files/file_storage/state_management.py +496 -0
  67. endoreg_db/import_files/file_storage/storage.py +36 -0
  68. endoreg_db/import_files/import_service.md +26 -0
  69. endoreg_db/import_files/processing/__init__.py +11 -0
  70. endoreg_db/import_files/processing/report_processing/report_anonymization.py +94 -0
  71. endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
  72. endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
  73. endoreg_db/import_files/pseudonymization/fake.py +52 -0
  74. endoreg_db/import_files/pseudonymization/k_anonymity.py +182 -0
  75. endoreg_db/import_files/pseudonymization/k_pseudonymity.py +128 -0
  76. endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
  77. endoreg_db/import_files/report_import_service.py +141 -0
  78. endoreg_db/import_files/video_import_service.py +150 -0
  79. endoreg_db/management/commands/import_report.py +130 -65
  80. endoreg_db/management/commands/import_video_with_classification.py +1 -1
  81. endoreg_db/management/commands/load_ai_model_data.py +5 -5
  82. endoreg_db/management/commands/load_ai_model_label_data.py +9 -7
  83. endoreg_db/management/commands/load_base_db_data.py +5 -134
  84. endoreg_db/management/commands/load_contraindication_data.py +14 -16
  85. endoreg_db/management/commands/load_disease_classification_choices_data.py +15 -18
  86. endoreg_db/management/commands/load_disease_classification_data.py +15 -18
  87. endoreg_db/management/commands/load_disease_data.py +25 -28
  88. endoreg_db/management/commands/load_endoscope_data.py +20 -27
  89. endoreg_db/management/commands/load_event_data.py +14 -16
  90. endoreg_db/management/commands/load_examination_data.py +31 -44
  91. endoreg_db/management/commands/load_examination_indication_data.py +20 -21
  92. endoreg_db/management/commands/load_finding_data.py +52 -80
  93. endoreg_db/management/commands/load_information_source.py +21 -23
  94. endoreg_db/management/commands/load_lab_value_data.py +17 -26
  95. endoreg_db/management/commands/load_medication_data.py +13 -12
  96. endoreg_db/management/commands/load_organ_data.py +15 -19
  97. endoreg_db/management/commands/load_pdf_type_data.py +19 -18
  98. endoreg_db/management/commands/load_profession_data.py +14 -17
  99. endoreg_db/management/commands/load_qualification_data.py +20 -23
  100. endoreg_db/management/commands/load_report_reader_flag_data.py +17 -19
  101. endoreg_db/management/commands/load_requirement_data.py +14 -20
  102. endoreg_db/management/commands/load_risk_data.py +7 -6
  103. endoreg_db/management/commands/load_shift_data.py +20 -23
  104. endoreg_db/management/commands/load_tag_data.py +8 -11
  105. endoreg_db/management/commands/load_unit_data.py +17 -19
  106. endoreg_db/management/commands/start_filewatcher.py +46 -37
  107. endoreg_db/management/commands/validate_video_files.py +1 -5
  108. endoreg_db/migrations/0001_initial.py +1360 -1812
  109. endoreg_db/models/administration/person/patient/patient.py +72 -46
  110. endoreg_db/models/label/__init__.py +2 -2
  111. endoreg_db/models/label/annotation/video_segmentation_annotation.py +18 -26
  112. endoreg_db/models/label/label_video_segment/label_video_segment.py +23 -1
  113. endoreg_db/models/media/pdf/raw_pdf.py +136 -64
  114. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +34 -10
  115. endoreg_db/models/media/processing_history/__init__.py +5 -0
  116. endoreg_db/models/media/processing_history/processing_history.py +96 -0
  117. endoreg_db/models/media/video/create_from_file.py +101 -31
  118. endoreg_db/models/media/video/video_file.py +125 -105
  119. endoreg_db/models/media/video/video_file_io.py +31 -26
  120. endoreg_db/models/medical/contraindication/README.md +1 -0
  121. endoreg_db/models/medical/examination/examination.py +28 -8
  122. endoreg_db/models/medical/examination/examination_indication.py +13 -79
  123. endoreg_db/models/medical/examination/examination_time.py +8 -3
  124. endoreg_db/models/medical/finding/finding.py +5 -12
  125. endoreg_db/models/medical/finding/finding_classification.py +18 -37
  126. endoreg_db/models/medical/finding/finding_intervention.py +7 -9
  127. endoreg_db/models/medical/hardware/endoscope.py +6 -0
  128. endoreg_db/models/medical/patient/medication_examples.py +5 -1
  129. endoreg_db/models/medical/patient/patient_finding.py +1 -1
  130. endoreg_db/models/metadata/pdf_meta.py +22 -10
  131. endoreg_db/models/metadata/sensitive_meta.py +3 -0
  132. endoreg_db/models/metadata/sensitive_meta_logic.py +200 -124
  133. endoreg_db/models/other/information_source.py +27 -6
  134. endoreg_db/models/report/__init__.py +0 -0
  135. endoreg_db/models/report/images.py +0 -0
  136. endoreg_db/models/report/report.py +6 -0
  137. endoreg_db/models/requirement/requirement.py +59 -399
  138. endoreg_db/models/requirement/requirement_operator.py +86 -98
  139. endoreg_db/models/state/audit_ledger.py +4 -5
  140. endoreg_db/models/state/raw_pdf.py +69 -30
  141. endoreg_db/models/state/video.py +65 -49
  142. endoreg_db/models/upload_job.py +33 -9
  143. endoreg_db/models/utils.py +27 -23
  144. endoreg_db/queries/__init__.py +3 -1
  145. endoreg_db/schemas/examination_evaluation.py +1 -1
  146. endoreg_db/serializers/__init__.py +2 -8
  147. endoreg_db/serializers/label_video_segment/label_video_segment.py +2 -29
  148. endoreg_db/serializers/meta/__init__.py +1 -6
  149. endoreg_db/serializers/misc/sensitive_patient_data.py +50 -26
  150. endoreg_db/serializers/patient_examination/patient_examination.py +3 -3
  151. endoreg_db/serializers/pdf/anony_text_validation.py +39 -23
  152. endoreg_db/serializers/video/video_file_list.py +65 -34
  153. endoreg_db/services/__old/pdf_import.py +1487 -0
  154. endoreg_db/services/__old/video_import.py +1306 -0
  155. endoreg_db/services/anonymization.py +63 -26
  156. endoreg_db/services/lookup_service.py +28 -28
  157. endoreg_db/services/lookup_store.py +2 -2
  158. endoreg_db/services/pdf_import.py +0 -1480
  159. endoreg_db/services/report_import.py +10 -0
  160. endoreg_db/services/video_import.py +6 -1165
  161. endoreg_db/tasks/upload_tasks.py +79 -70
  162. endoreg_db/tasks/video_ingest.py +8 -4
  163. endoreg_db/urls/__init__.py +0 -14
  164. endoreg_db/urls/ai.py +32 -0
  165. endoreg_db/urls/media.py +21 -24
  166. endoreg_db/utils/dataloader.py +87 -57
  167. endoreg_db/utils/paths.py +110 -46
  168. endoreg_db/utils/pipelines/Readme.md +1 -1
  169. endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +97 -0
  170. endoreg_db/utils/video/ffmpeg_wrapper.py +217 -52
  171. endoreg_db/views/__init__.py +85 -173
  172. endoreg_db/views/ai/__init__.py +8 -0
  173. endoreg_db/views/ai/label.py +155 -0
  174. endoreg_db/views/anonymization/media_management.py +8 -7
  175. endoreg_db/views/anonymization/overview.py +97 -68
  176. endoreg_db/views/anonymization/validate.py +25 -21
  177. endoreg_db/views/media/__init__.py +5 -20
  178. endoreg_db/views/media/pdf_media.py +109 -65
  179. endoreg_db/views/media/sensitive_metadata.py +163 -148
  180. endoreg_db/views/meta/__init__.py +0 -8
  181. endoreg_db/views/misc/__init__.py +1 -7
  182. endoreg_db/views/misc/upload_views.py +94 -93
  183. endoreg_db/views/report/__init__.py +7 -0
  184. endoreg_db/views/{pdf → report}/reimport.py +45 -24
  185. endoreg_db/views/{pdf/pdf_stream.py → report/report_stream.py} +40 -32
  186. endoreg_db/views/requirement/lookup_store.py +22 -90
  187. endoreg_db/views/video/__init__.py +23 -22
  188. endoreg_db/views/video/correction.py +201 -172
  189. endoreg_db/views/video/reimport.py +1 -1
  190. endoreg_db/views/{media/video_segments.py → video/segments_crud.py} +75 -37
  191. endoreg_db/views/video/{video_meta.py → video_meta_stats.py} +2 -2
  192. endoreg_db/views/video/video_stream.py +7 -8
  193. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/METADATA +2 -2
  194. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/RECORD +217 -335
  195. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/WHEEL +1 -1
  196. endoreg_db/data/_examples/disease.yaml +0 -55
  197. endoreg_db/data/_examples/disease_classification.yaml +0 -13
  198. endoreg_db/data/_examples/disease_classification_choice.yaml +0 -62
  199. endoreg_db/data/_examples/event.yaml +0 -64
  200. endoreg_db/data/_examples/examination.yaml +0 -72
  201. endoreg_db/data/_examples/finding/anatomy_colon.yaml +0 -128
  202. endoreg_db/data/_examples/finding/colonoscopy.yaml +0 -40
  203. endoreg_db/data/_examples/finding/colonoscopy_bowel_prep.yaml +0 -56
  204. endoreg_db/data/_examples/finding/complication.yaml +0 -16
  205. endoreg_db/data/_examples/finding/data.yaml +0 -105
  206. endoreg_db/data/_examples/finding/examination_setting.yaml +0 -16
  207. endoreg_db/data/_examples/finding/medication_related.yaml +0 -18
  208. endoreg_db/data/_examples/finding/outcome.yaml +0 -12
  209. endoreg_db/data/_examples/finding_classification/colonoscopy_bowel_preparation.yaml +0 -68
  210. endoreg_db/data/_examples/finding_classification/colonoscopy_jnet.yaml +0 -22
  211. endoreg_db/data/_examples/finding_classification/colonoscopy_kudo.yaml +0 -25
  212. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
  213. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
  214. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_size.yaml +0 -68
  215. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
  216. endoreg_db/data/_examples/finding_classification/colonoscopy_location.yaml +0 -80
  217. endoreg_db/data/_examples/finding_classification/colonoscopy_lst.yaml +0 -21
  218. endoreg_db/data/_examples/finding_classification/colonoscopy_nice.yaml +0 -20
  219. endoreg_db/data/_examples/finding_classification/colonoscopy_paris.yaml +0 -26
  220. endoreg_db/data/_examples/finding_classification/colonoscopy_sano.yaml +0 -22
  221. endoreg_db/data/_examples/finding_classification/colonoscopy_summary.yaml +0 -53
  222. endoreg_db/data/_examples/finding_classification/complication_generic.yaml +0 -25
  223. endoreg_db/data/_examples/finding_classification/examination_setting_generic.yaml +0 -40
  224. endoreg_db/data/_examples/finding_classification/histology_colo.yaml +0 -51
  225. endoreg_db/data/_examples/finding_classification/intervention_required.yaml +0 -26
  226. endoreg_db/data/_examples/finding_classification/medication_related.yaml +0 -23
  227. endoreg_db/data/_examples/finding_classification/visualized.yaml +0 -33
  228. endoreg_db/data/_examples/finding_classification_choice/bowel_preparation.yaml +0 -78
  229. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
  230. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
  231. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
  232. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_lst.yaml +0 -15
  233. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_nice.yaml +0 -17
  234. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
  235. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_sano.yaml +0 -14
  236. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
  237. endoreg_db/data/_examples/finding_classification_choice/colonoscopy_size.yaml +0 -82
  238. endoreg_db/data/_examples/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
  239. endoreg_db/data/_examples/finding_classification_choice/complication_generic_types.yaml +0 -15
  240. endoreg_db/data/_examples/finding_classification_choice/examination_setting_generic_types.yaml +0 -15
  241. endoreg_db/data/_examples/finding_classification_choice/histology.yaml +0 -24
  242. endoreg_db/data/_examples/finding_classification_choice/histology_polyp.yaml +0 -20
  243. endoreg_db/data/_examples/finding_classification_choice/outcome.yaml +0 -19
  244. endoreg_db/data/_examples/finding_classification_choice/yes_no_na.yaml +0 -11
  245. endoreg_db/data/_examples/finding_classification_type/colonoscopy_basic.yaml +0 -48
  246. endoreg_db/data/_examples/finding_intervention/endoscopy.yaml +0 -43
  247. endoreg_db/data/_examples/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
  248. endoreg_db/data/_examples/finding_intervention/endoscopy_egd.yaml +0 -128
  249. endoreg_db/data/_examples/finding_intervention/endoscopy_ercp.yaml +0 -32
  250. endoreg_db/data/_examples/finding_intervention/endoscopy_eus_lower.yaml +0 -9
  251. endoreg_db/data/_examples/finding_intervention/endoscopy_eus_upper.yaml +0 -36
  252. endoreg_db/data/_examples/finding_intervention_type/endoscopy.yaml +0 -15
  253. endoreg_db/data/_examples/finding_type/data.yaml +0 -43
  254. endoreg_db/data/_examples/requirement/age.yaml +0 -26
  255. endoreg_db/data/_examples/requirement/gender.yaml +0 -25
  256. endoreg_db/data/_examples/requirement_set/01_endoscopy_generic.yaml +0 -48
  257. endoreg_db/data/_examples/requirement_set/colonoscopy_austria_screening.yaml +0 -57
  258. endoreg_db/data/_examples/requirement_set/endoscopy_bleeding_risk.yaml +0 -52
  259. endoreg_db/data/_examples/yaml_examples.xlsx +0 -0
  260. endoreg_db/data/finding/anatomy_colon.yaml +0 -128
  261. endoreg_db/data/finding/colonoscopy.yaml +0 -40
  262. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +0 -56
  263. endoreg_db/data/finding/complication.yaml +0 -16
  264. endoreg_db/data/finding/data.yaml +0 -105
  265. endoreg_db/data/finding/examination_setting.yaml +0 -16
  266. endoreg_db/data/finding/medication_related.yaml +0 -18
  267. endoreg_db/data/finding/outcome.yaml +0 -12
  268. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +0 -22
  269. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +0 -25
  270. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
  271. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
  272. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +0 -38
  273. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
  274. endoreg_db/data/finding_classification/colonoscopy_location.yaml +0 -49
  275. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +0 -21
  276. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +0 -20
  277. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +0 -26
  278. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +0 -22
  279. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +0 -53
  280. endoreg_db/data/finding_classification/complication_generic.yaml +0 -25
  281. endoreg_db/data/finding_classification/examination_setting_generic.yaml +0 -40
  282. endoreg_db/data/finding_classification/histology_colo.yaml +0 -43
  283. endoreg_db/data/finding_classification/intervention_required.yaml +0 -26
  284. endoreg_db/data/finding_classification/medication_related.yaml +0 -23
  285. endoreg_db/data/finding_classification/visualized.yaml +0 -33
  286. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
  287. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
  288. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
  289. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +0 -15
  290. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +0 -17
  291. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +0 -57
  292. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
  293. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +0 -14
  294. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
  295. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +0 -229
  296. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +0 -19
  297. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +0 -82
  298. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
  299. endoreg_db/data/finding_classification_choice/outcome.yaml +0 -19
  300. endoreg_db/data/finding_intervention/endoscopy.yaml +0 -43
  301. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
  302. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +0 -128
  303. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +0 -32
  304. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +0 -9
  305. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +0 -36
  306. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +0 -79
  307. endoreg_db/data/requirement/age.yaml +0 -26
  308. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +0 -45
  309. endoreg_db/data/requirement/disease_cardiovascular.yaml +0 -79
  310. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +0 -41
  311. endoreg_db/data/requirement/disease_hepatology.yaml +0 -12
  312. endoreg_db/data/requirement/disease_misc.yaml +0 -12
  313. endoreg_db/data/requirement/disease_renal.yaml +0 -96
  314. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +0 -59
  315. endoreg_db/data/requirement/event_cardiology.yaml +0 -251
  316. endoreg_db/data/requirement/event_requirements.yaml +0 -145
  317. endoreg_db/data/requirement/finding_colon_polyp.yaml +0 -50
  318. endoreg_db/data/requirement/gender.yaml +0 -25
  319. endoreg_db/data/requirement/lab_value.yaml +0 -441
  320. endoreg_db/data/requirement/medication.yaml +0 -93
  321. endoreg_db/data/requirement_operator/age.yaml +0 -13
  322. endoreg_db/data/requirement_operator/lab_operators.yaml +0 -129
  323. endoreg_db/data/requirement_operator/model_operators.yaml +0 -96
  324. endoreg_db/management/commands/init_default_ai_model.py +0 -112
  325. endoreg_db/management/commands/reset_celery_schedule.py +0 -9
  326. endoreg_db/management/commands/validate_video.py +0 -204
  327. endoreg_db/migrations/0002_requirementset_depends_on.py +0 -18
  328. endoreg_db/migrations/_old/0001_initial.py +0 -1857
  329. endoreg_db/migrations/_old/0002_add_video_correction_models.py +0 -52
  330. endoreg_db/migrations/_old/0003_add_center_display_name.py +0 -30
  331. endoreg_db/migrations/_old/0004_employee_city_employee_post_code_employee_street_and_more.py +0 -68
  332. endoreg_db/migrations/_old/0004_remove_casetemplate_rules_and_more.py +0 -77
  333. endoreg_db/migrations/_old/0005_merge_20251111_1003.py +0 -14
  334. endoreg_db/migrations/_old/0006_sensitivemeta_anonymized_text_and_more.py +0 -68
  335. endoreg_db/migrations/_old/0007_remove_rule_attribute_dtype_remove_rule_rule_type_and_more.py +0 -89
  336. endoreg_db/migrations/_old/0008_remove_event_event_classification_and_more.py +0 -27
  337. endoreg_db/migrations/_old/0009_alter_modelmeta_options_and_more.py +0 -21
  338. endoreg_db/renames.yml +0 -8
  339. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +0 -223
  340. endoreg_db/serializers/_old/raw_video_meta_validation.py +0 -179
  341. endoreg_db/serializers/_old/video.py +0 -71
  342. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +0 -115
  343. endoreg_db/serializers/meta/report_meta.py +0 -53
  344. endoreg_db/serializers/report/__init__.py +0 -9
  345. endoreg_db/serializers/report/mixins.py +0 -45
  346. endoreg_db/serializers/report/report.py +0 -105
  347. endoreg_db/serializers/report/report_list.py +0 -22
  348. endoreg_db/serializers/report/secure_file_url.py +0 -26
  349. endoreg_db/services/requirements_object.py +0 -147
  350. endoreg_db/services/storage_aware_video_processor.py +0 -370
  351. endoreg_db/urls/files.py +0 -6
  352. endoreg_db/urls/label_video_segment_validate.py +0 -33
  353. endoreg_db/urls/label_video_segments.py +0 -46
  354. endoreg_db/views/label/__init__.py +0 -5
  355. endoreg_db/views/label/label.py +0 -15
  356. endoreg_db/views/label_video_segment/__init__.py +0 -16
  357. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +0 -44
  358. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +0 -50
  359. endoreg_db/views/label_video_segment/label_video_segment.py +0 -77
  360. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +0 -174
  361. endoreg_db/views/label_video_segment/label_video_segment_detail.py +0 -73
  362. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +0 -46
  363. endoreg_db/views/label_video_segment/validate.py +0 -226
  364. endoreg_db/views/media/segments.py +0 -71
  365. endoreg_db/views/meta/available_files_list.py +0 -146
  366. endoreg_db/views/meta/report_meta.py +0 -53
  367. endoreg_db/views/meta/sensitive_meta_detail.py +0 -85
  368. endoreg_db/views/misc/secure_file_serving_view.py +0 -80
  369. endoreg_db/views/misc/secure_file_url_view.py +0 -84
  370. endoreg_db/views/misc/secure_url_validate.py +0 -79
  371. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +0 -164
  372. endoreg_db/views/patient_finding_location/__init__.py +0 -5
  373. endoreg_db/views/patient_finding_location/pfl_create.py +0 -70
  374. endoreg_db/views/patient_finding_morphology/__init__.py +0 -5
  375. endoreg_db/views/patient_finding_morphology/pfm_create.py +0 -70
  376. endoreg_db/views/pdf/__init__.py +0 -8
  377. endoreg_db/views/video/segmentation.py +0 -274
  378. endoreg_db/views/video/task_status.py +0 -49
  379. endoreg_db/views/video/timeline.py +0 -46
  380. endoreg_db/views/video/video_analyze.py +0 -52
  381. /endoreg_db/data/requirement/{colon_polyp_intervention.yaml → old/colon_polyp_intervention.yaml} +0 -0
  382. /endoreg_db/data/{_examples/requirement → requirement/old}/colonoscopy_baseline_austria.yaml +0 -0
  383. /endoreg_db/data/requirement/{coloreg_colon_polyp.yaml → old/coloreg_colon_polyp.yaml} +0 -0
  384. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_cardiovascular.yaml +0 -0
  385. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_classification_choice_cardiovascular.yaml +0 -0
  386. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_hepatology.yaml +0 -0
  387. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_misc.yaml +0 -0
  388. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_renal.yaml +0 -0
  389. /endoreg_db/data/{_examples/requirement → requirement/old}/endoscopy_bleeding_risk.yaml +0 -0
  390. /endoreg_db/data/{_examples/requirement → requirement/old}/event_cardiology.yaml +0 -0
  391. /endoreg_db/data/{_examples/requirement → requirement/old}/event_requirements.yaml +0 -0
  392. /endoreg_db/data/{_examples/requirement → requirement/old}/finding_colon_polyp.yaml +0 -0
  393. /endoreg_db/{urls/sensitive_meta.py → data/requirement/old/gender.yaml} +0 -0
  394. /endoreg_db/data/{_examples/requirement → requirement/old}/lab_value.yaml +0 -0
  395. /endoreg_db/data/{_examples/requirement → requirement/old}/medication.yaml +0 -0
  396. /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/age.yaml +0 -0
  397. /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/lab_operators.yaml +0 -0
  398. /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/model_operators.yaml +0 -0
  399. /endoreg_db/{views/pdf/pdf_stream_views.py → import_files/pseudonymization/__init__.py} +0 -0
  400. /endoreg_db/utils/requirement_operator_logic/{lab_value_operators.py → _old/lab_value_operators.py} +0 -0
  401. /endoreg_db/utils/requirement_operator_logic/{model_evaluators.py → _old/model_evaluators.py} +0 -0
  402. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/licenses/LICENSE +0 -0
@@ -7,12 +7,12 @@ from typing import TYPE_CHECKING, Optional, Type
7
7
 
8
8
  # Import the new exceptions from the correct path
9
9
  from endoreg_db.exceptions import InsufficientStorageError, TranscodingError
10
-
11
- from ...utils import TMP_VIDEO_DIR, VIDEO_DIR
10
+ from endoreg_db.utils.paths import IMPORT_VIDEO_DIR, SENSITIVE_VIDEO_DIR, TRANSCODING_DIR
12
11
 
13
12
  if TYPE_CHECKING:
14
13
  from endoreg_db.models import VideoFile
15
14
 
15
+ import endoreg_db.utils.paths as path_utils
16
16
  from ....utils.file_operations import get_uuid_filename
17
17
  from ....utils.hashs import get_video_hash
18
18
  from ....utils.video.ffmpeg_wrapper import transcode_videofile_if_required
@@ -20,7 +20,9 @@ from ....utils.video.ffmpeg_wrapper import transcode_videofile_if_required
20
20
  logger = logging.getLogger(__name__)
21
21
 
22
22
 
23
- def check_storage_capacity(src_path: Path, dst_root: Path, safety_margin: float = 1.2) -> None:
23
+ def check_storage_capacity(
24
+ src_path: Path, dst_root: Path, safety_margin: float = 1.2
25
+ ) -> None:
24
26
  """
25
27
  Check if there's enough storage space before starting operations.
26
28
 
@@ -46,14 +48,16 @@ def check_storage_capacity(src_path: Path, dst_root: Path, safety_margin: float
46
48
  available_space=free_space,
47
49
  )
48
50
 
49
- logger.info(f"Storage check passed: {free_space / 1e9:.1f} GB available, {required_space / 1e9:.1f} GB required")
51
+ logger.info(
52
+ f"Storage check passed: {free_space / 1e9:.1f} GB available, {required_space / 1e9:.1f} GB required"
53
+ )
50
54
 
51
55
  except OSError as e:
52
56
  logger.warning(f"Could not check storage capacity: {e}")
53
57
  # Don't fail the operation, just log the warning
54
58
 
55
59
 
56
- def atomic_copy_with_fallback(src_path: Path, dst_path: Path) -> bool:
60
+ def atomic_copy_with_fallback(src_path: Path = IMPORT_VIDEO_DIR, dst_path: Path = SENSITIVE_VIDEO_DIR) -> bool:
57
61
  """
58
62
  Atomically copy file from src to dst, preserving the source file.
59
63
 
@@ -157,7 +161,9 @@ def atomic_move_with_fallback(src_path: Path, dst_path: Path) -> bool:
157
161
  # Re-raise with better context
158
162
  if e.errno == 28: # No space left on device
159
163
  raise InsufficientStorageError(
160
- f"No space left on device during copy: {e}", required_space=src_path.stat().st_size, available_space=shutil.disk_usage(dst_path.parent).free
164
+ f"No space left on device during copy: {e}",
165
+ required_space=src_path.stat().st_size,
166
+ available_space=shutil.disk_usage(dst_path.parent).free,
161
167
  )
162
168
  raise
163
169
 
@@ -187,7 +193,7 @@ def _create_from_file(
187
193
  file_path: Path,
188
194
  center_name: str,
189
195
  processor_name: Optional[str] = None,
190
- video_dir: Path = VIDEO_DIR,
196
+ video_dir: Path = IMPORT_VIDEO_DIR,
191
197
  save: bool = True,
192
198
  delete_source: bool = False,
193
199
  **kwargs,
@@ -224,16 +230,22 @@ def _create_from_file(
224
230
 
225
231
  # 1. Transcode if necessary
226
232
  logger.debug("Checking transcoding requirement for %s", file_path)
227
- temp_transcode_dir = TMP_VIDEO_DIR / "transcoding"
233
+ temp_transcode_dir = TRANSCODING_DIR
228
234
  temp_transcode_dir.mkdir(parents=True, exist_ok=True)
229
235
 
230
236
  # Use a unique name for the potential transcoded file
231
- temp_transcoded_output_path = temp_transcode_dir / f"{uuid.uuid4()}{original_suffix}"
237
+ temp_transcoded_output_path = (
238
+ temp_transcode_dir / f"{uuid.uuid4()}{original_suffix}"
239
+ )
232
240
 
233
241
  try:
234
- transcoded_file_path = transcode_videofile_if_required(input_path=file_path, output_path=temp_transcoded_output_path)
242
+ transcoded_file_path = transcode_videofile_if_required(
243
+ input_path=file_path, output_path=temp_transcoded_output_path
244
+ )
235
245
  if transcoded_file_path is None:
236
- raise TranscodingError(f"Transcoding check/process failed for {file_path}")
246
+ raise TranscodingError(
247
+ f"Transcoding check/process failed for {file_path}"
248
+ )
237
249
  except Exception as e:
238
250
  raise TranscodingError(f"Video transcoding failed: {e}") from e
239
251
 
@@ -242,24 +254,42 @@ def _create_from_file(
242
254
  # 2. Calculate hash (this will be the raw_video_hash)
243
255
  video_hash = get_video_hash(transcoded_file_path)
244
256
  if not video_hash:
245
- raise ValueError(f"Could not calculate video hash for {transcoded_file_path}")
246
- logger.info("Calculated raw video hash: %s for %s", video_hash, original_file_name)
257
+ raise ValueError(
258
+ f"Could not calculate video hash for {transcoded_file_path}"
259
+ )
260
+ logger.info(
261
+ "Calculated raw video hash: %s for %s", video_hash, original_file_name
262
+ )
247
263
 
248
264
  # 3. Check if hash already exists
249
265
  if cls_model.check_hash_exists(video_hash=video_hash):
250
266
  existing_video = cls_model.objects.get(video_hash=video_hash)
251
- logger.warning("Video with hash %s already exists (UUID: %s)", video_hash, existing_video.uuid)
267
+ logger.warning(
268
+ "Video with hash %s already exists (UUID: %s)",
269
+ video_hash,
270
+ existing_video.uuid,
271
+ )
252
272
 
253
273
  # Check if the existing video has a valid file
254
274
  existing_raw_path = existing_video.get_raw_file_path()
255
- if existing_video.has_raw and existing_raw_path and existing_raw_path.exists():
256
- logger.warning("Video with hash %s already exists and file is present. Returning existing instance.", video_hash)
275
+ if (
276
+ existing_video.has_raw
277
+ and existing_raw_path
278
+ and existing_raw_path.exists()
279
+ ):
280
+ logger.warning(
281
+ "Video with hash %s already exists and file is present. Returning existing instance.",
282
+ video_hash,
283
+ )
257
284
  # Clean up transcoded file if it was created temporarily
258
285
  if transcoded_file_path != file_path and transcoded_file_path.exists():
259
286
  transcoded_file_path.unlink(missing_ok=True)
260
287
  return existing_video
261
288
 
262
- logger.warning("Video with hash %s exists but file is missing. Deleting orphaned record.", video_hash)
289
+ logger.warning(
290
+ "Video with hash %s exists but file is missing. Deleting orphaned record.",
291
+ video_hash,
292
+ )
263
293
  existing_video.delete()
264
294
 
265
295
  # 4. Generate UUID and final storage path
@@ -270,16 +300,26 @@ def _create_from_file(
270
300
  # 5. Move or Copy the file to final storage using improved method
271
301
  try:
272
302
  if delete_source and transcoded_file_path == file_path:
273
- logger.debug("Moving original file %s to %s", file_path, final_storage_path)
303
+ logger.debug(
304
+ "Moving original file %s to %s", file_path, final_storage_path
305
+ )
274
306
  atomic_move_with_fallback(file_path, final_storage_path)
275
307
  elif delete_source and transcoded_file_path != file_path:
276
- logger.debug("Moving transcoded file %s to %s", transcoded_file_path, final_storage_path)
308
+ logger.debug(
309
+ "Moving transcoded file %s to %s",
310
+ transcoded_file_path,
311
+ final_storage_path,
312
+ )
277
313
  atomic_move_with_fallback(transcoded_file_path, final_storage_path)
278
314
  else:
279
- logger.debug("Copying file %s to %s", transcoded_file_path, final_storage_path)
315
+ logger.debug(
316
+ "Copying file %s to %s", transcoded_file_path, final_storage_path
317
+ )
280
318
  atomic_copy_with_fallback(transcoded_file_path, final_storage_path)
281
319
  if transcoded_file_path != file_path and transcoded_file_path.exists():
282
- logger.debug("Cleaning up temporary transcoded file %s", transcoded_file_path)
320
+ logger.debug(
321
+ "Cleaning up temporary transcoded file %s", transcoded_file_path
322
+ )
283
323
  transcoded_file_path.unlink(missing_ok=True)
284
324
  except InsufficientStorageError:
285
325
  # Re-raise storage errors as-is
@@ -290,15 +330,29 @@ def _create_from_file(
290
330
  # 6. Verify hash after move/copy
291
331
  final_hash = get_video_hash(final_storage_path)
292
332
  if final_hash != video_hash:
293
- logger.error("Hash mismatch after file operation! Expected %s, got %s", video_hash, final_hash)
333
+ logger.error(
334
+ "Hash mismatch after file operation! Expected %s, got %s",
335
+ video_hash,
336
+ final_hash,
337
+ )
294
338
  final_storage_path.unlink(missing_ok=True)
295
- raise RuntimeError(f"Hash mismatch after file operation for {final_storage_path}")
339
+ raise RuntimeError(
340
+ f"Hash mismatch after file operation for {final_storage_path}"
341
+ )
296
342
 
297
343
  # 7. Get related objects
298
344
  try:
299
345
  center = Center.objects.get(name=center_name)
300
- processor = EndoscopyProcessor.objects.get(name=processor_name) if processor_name else None
301
- logger.debug("Found Center: %s, Processor: %s", center.name, processor.name if processor else "None")
346
+ processor = (
347
+ EndoscopyProcessor.objects.get(name=processor_name)
348
+ if processor_name
349
+ else None
350
+ )
351
+ logger.debug(
352
+ "Found Center: %s, Processor: %s",
353
+ center.name,
354
+ processor.name if processor else "None",
355
+ )
302
356
  except Center.DoesNotExist as e:
303
357
  logger.error("Center '%s' not found", center_name)
304
358
  if final_storage_path and final_storage_path.exists():
@@ -313,8 +367,10 @@ def _create_from_file(
313
367
  # 8. Create the VideoFile instance
314
368
  logger.info("Creating new VideoFile instance with UUID: %s", uuid_val)
315
369
  # Store FileField path relative to storage root including the videos prefix
316
- storage_base = Path(_get_path(data_paths, "storage", final_storage_path.parent))
317
- relative_name = (final_storage_path.relative_to(storage_base)).as_posix()
370
+ # TODO Review removal, since this is now newly handled by path_utils
371
+ #storage_base = Path(_get_path(data_paths, "storage", final_storage_path.parent))
372
+
373
+ relative_name = path_utils.to_storage_relative(final_storage_path)
318
374
  video = cls_model(
319
375
  uuid=uuid_val,
320
376
  raw_file=relative_name,
@@ -331,7 +387,9 @@ def _create_from_file(
331
387
  if save:
332
388
  logger.info("Saving new VideoFile instance (UUID: %s)", uuid_val)
333
389
  video.save()
334
- logger.info("Successfully created VideoFile PK %s (UUID: %s)", video.pk, video.uuid)
390
+ logger.info(
391
+ "Successfully created VideoFile PK %s (UUID: %s)", video.pk, video.uuid
392
+ )
335
393
 
336
394
  return video
337
395
 
@@ -339,12 +397,24 @@ def _create_from_file(
339
397
  # Re-raise these specific errors as-is
340
398
  raise
341
399
  except Exception as e:
342
- logger.error("Failed to create VideoFile from %s: (%s) %s", file_path, type(e).__name__, e, exc_info=True)
400
+ logger.error(
401
+ "Failed to create VideoFile from %s: (%s) %s",
402
+ file_path,
403
+ type(e).__name__,
404
+ e,
405
+ exc_info=True,
406
+ )
343
407
  # Clean up any created files
344
408
  if final_storage_path and final_storage_path.exists():
345
409
  logger.warning("Cleaning up orphaned file: %s", final_storage_path)
346
410
  final_storage_path.unlink(missing_ok=True)
347
- if transcoded_file_path and transcoded_file_path != file_path and transcoded_file_path.exists():
348
- logger.warning("Cleaning up orphaned transcoded file: %s", transcoded_file_path)
411
+ if (
412
+ transcoded_file_path
413
+ and transcoded_file_path != file_path
414
+ and transcoded_file_path.exists()
415
+ ):
416
+ logger.warning(
417
+ "Cleaning up orphaned transcoded file: %s", transcoded_file_path
418
+ )
349
419
  transcoded_file_path.unlink(missing_ok=True)
350
420
  raise RuntimeError(f"Video processing failed: {e}") from e