endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

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  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 +400 -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/processing/video_processing/video_cleanup_on_error.py +119 -0
  74. endoreg_db/import_files/pseudonymization/fake.py +52 -0
  75. endoreg_db/import_files/pseudonymization/k_anonymity.py +182 -0
  76. endoreg_db/import_files/pseudonymization/k_pseudonymity.py +128 -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 +64 -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/views/__init__.py +85 -173
  171. endoreg_db/views/ai/__init__.py +8 -0
  172. endoreg_db/views/ai/label.py +155 -0
  173. endoreg_db/views/anonymization/media_management.py +8 -7
  174. endoreg_db/views/anonymization/overview.py +97 -68
  175. endoreg_db/views/anonymization/validate.py +25 -21
  176. endoreg_db/views/media/__init__.py +5 -20
  177. endoreg_db/views/media/pdf_media.py +109 -65
  178. endoreg_db/views/media/sensitive_metadata.py +163 -148
  179. endoreg_db/views/meta/__init__.py +0 -8
  180. endoreg_db/views/misc/__init__.py +1 -7
  181. endoreg_db/views/misc/upload_views.py +94 -93
  182. endoreg_db/views/report/__init__.py +7 -0
  183. endoreg_db/views/{pdf → report}/reimport.py +45 -24
  184. endoreg_db/views/{pdf/pdf_stream.py → report/report_stream.py} +40 -32
  185. endoreg_db/views/requirement/lookup_store.py +22 -90
  186. endoreg_db/views/video/__init__.py +23 -22
  187. endoreg_db/views/video/correction.py +201 -172
  188. endoreg_db/views/video/reimport.py +1 -1
  189. endoreg_db/views/{media/video_segments.py → video/segments_crud.py} +75 -37
  190. endoreg_db/views/video/{video_meta.py → video_meta_stats.py} +2 -2
  191. endoreg_db/views/video/video_stream.py +7 -8
  192. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.8.9.dist-info}/METADATA +2 -2
  193. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.8.9.dist-info}/RECORD +217 -335
  194. {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.8.9.dist-info}/WHEEL +1 -1
  195. endoreg_db/data/_examples/disease.yaml +0 -55
  196. endoreg_db/data/_examples/disease_classification.yaml +0 -13
  197. endoreg_db/data/_examples/disease_classification_choice.yaml +0 -62
  198. endoreg_db/data/_examples/event.yaml +0 -64
  199. endoreg_db/data/_examples/examination.yaml +0 -72
  200. endoreg_db/data/_examples/finding/anatomy_colon.yaml +0 -128
  201. endoreg_db/data/_examples/finding/colonoscopy.yaml +0 -40
  202. endoreg_db/data/_examples/finding/colonoscopy_bowel_prep.yaml +0 -56
  203. endoreg_db/data/_examples/finding/complication.yaml +0 -16
  204. endoreg_db/data/_examples/finding/data.yaml +0 -105
  205. endoreg_db/data/_examples/finding/examination_setting.yaml +0 -16
  206. endoreg_db/data/_examples/finding/medication_related.yaml +0 -18
  207. endoreg_db/data/_examples/finding/outcome.yaml +0 -12
  208. endoreg_db/data/_examples/finding_classification/colonoscopy_bowel_preparation.yaml +0 -68
  209. endoreg_db/data/_examples/finding_classification/colonoscopy_jnet.yaml +0 -22
  210. endoreg_db/data/_examples/finding_classification/colonoscopy_kudo.yaml +0 -25
  211. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
  212. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
  213. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_size.yaml +0 -68
  214. endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
  215. endoreg_db/data/_examples/finding_classification/colonoscopy_location.yaml +0 -80
  216. endoreg_db/data/_examples/finding_classification/colonoscopy_lst.yaml +0 -21
  217. endoreg_db/data/_examples/finding_classification/colonoscopy_nice.yaml +0 -20
  218. endoreg_db/data/_examples/finding_classification/colonoscopy_paris.yaml +0 -26
  219. endoreg_db/data/_examples/finding_classification/colonoscopy_sano.yaml +0 -22
  220. endoreg_db/data/_examples/finding_classification/colonoscopy_summary.yaml +0 -53
  221. endoreg_db/data/_examples/finding_classification/complication_generic.yaml +0 -25
  222. endoreg_db/data/_examples/finding_classification/examination_setting_generic.yaml +0 -40
  223. endoreg_db/data/_examples/finding_classification/histology_colo.yaml +0 -51
  224. endoreg_db/data/_examples/finding_classification/intervention_required.yaml +0 -26
  225. endoreg_db/data/_examples/finding_classification/medication_related.yaml +0 -23
  226. endoreg_db/data/_examples/finding_classification/visualized.yaml +0 -33
  227. endoreg_db/data/_examples/finding_classification_choice/bowel_preparation.yaml +0 -78
  228. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
  229. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
  230. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
  231. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_lst.yaml +0 -15
  232. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_nice.yaml +0 -17
  233. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
  234. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_sano.yaml +0 -14
  235. endoreg_db/data/_examples/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
  236. endoreg_db/data/_examples/finding_classification_choice/colonoscopy_size.yaml +0 -82
  237. endoreg_db/data/_examples/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
  238. endoreg_db/data/_examples/finding_classification_choice/complication_generic_types.yaml +0 -15
  239. endoreg_db/data/_examples/finding_classification_choice/examination_setting_generic_types.yaml +0 -15
  240. endoreg_db/data/_examples/finding_classification_choice/histology.yaml +0 -24
  241. endoreg_db/data/_examples/finding_classification_choice/histology_polyp.yaml +0 -20
  242. endoreg_db/data/_examples/finding_classification_choice/outcome.yaml +0 -19
  243. endoreg_db/data/_examples/finding_classification_choice/yes_no_na.yaml +0 -11
  244. endoreg_db/data/_examples/finding_classification_type/colonoscopy_basic.yaml +0 -48
  245. endoreg_db/data/_examples/finding_intervention/endoscopy.yaml +0 -43
  246. endoreg_db/data/_examples/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
  247. endoreg_db/data/_examples/finding_intervention/endoscopy_egd.yaml +0 -128
  248. endoreg_db/data/_examples/finding_intervention/endoscopy_ercp.yaml +0 -32
  249. endoreg_db/data/_examples/finding_intervention/endoscopy_eus_lower.yaml +0 -9
  250. endoreg_db/data/_examples/finding_intervention/endoscopy_eus_upper.yaml +0 -36
  251. endoreg_db/data/_examples/finding_intervention_type/endoscopy.yaml +0 -15
  252. endoreg_db/data/_examples/finding_type/data.yaml +0 -43
  253. endoreg_db/data/_examples/requirement/age.yaml +0 -26
  254. endoreg_db/data/_examples/requirement/gender.yaml +0 -25
  255. endoreg_db/data/_examples/requirement_set/01_endoscopy_generic.yaml +0 -48
  256. endoreg_db/data/_examples/requirement_set/colonoscopy_austria_screening.yaml +0 -57
  257. endoreg_db/data/_examples/requirement_set/endoscopy_bleeding_risk.yaml +0 -52
  258. endoreg_db/data/_examples/yaml_examples.xlsx +0 -0
  259. endoreg_db/data/finding/anatomy_colon.yaml +0 -128
  260. endoreg_db/data/finding/colonoscopy.yaml +0 -40
  261. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +0 -56
  262. endoreg_db/data/finding/complication.yaml +0 -16
  263. endoreg_db/data/finding/data.yaml +0 -105
  264. endoreg_db/data/finding/examination_setting.yaml +0 -16
  265. endoreg_db/data/finding/medication_related.yaml +0 -18
  266. endoreg_db/data/finding/outcome.yaml +0 -12
  267. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +0 -22
  268. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +0 -25
  269. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
  270. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
  271. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +0 -38
  272. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
  273. endoreg_db/data/finding_classification/colonoscopy_location.yaml +0 -49
  274. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +0 -21
  275. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +0 -20
  276. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +0 -26
  277. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +0 -22
  278. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +0 -53
  279. endoreg_db/data/finding_classification/complication_generic.yaml +0 -25
  280. endoreg_db/data/finding_classification/examination_setting_generic.yaml +0 -40
  281. endoreg_db/data/finding_classification/histology_colo.yaml +0 -43
  282. endoreg_db/data/finding_classification/intervention_required.yaml +0 -26
  283. endoreg_db/data/finding_classification/medication_related.yaml +0 -23
  284. endoreg_db/data/finding_classification/visualized.yaml +0 -33
  285. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
  286. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
  287. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
  288. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +0 -15
  289. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +0 -17
  290. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +0 -57
  291. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
  292. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +0 -14
  293. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
  294. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +0 -229
  295. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +0 -19
  296. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +0 -82
  297. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
  298. endoreg_db/data/finding_classification_choice/outcome.yaml +0 -19
  299. endoreg_db/data/finding_intervention/endoscopy.yaml +0 -43
  300. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
  301. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +0 -128
  302. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +0 -32
  303. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +0 -9
  304. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +0 -36
  305. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +0 -79
  306. endoreg_db/data/requirement/age.yaml +0 -26
  307. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +0 -45
  308. endoreg_db/data/requirement/disease_cardiovascular.yaml +0 -79
  309. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +0 -41
  310. endoreg_db/data/requirement/disease_hepatology.yaml +0 -12
  311. endoreg_db/data/requirement/disease_misc.yaml +0 -12
  312. endoreg_db/data/requirement/disease_renal.yaml +0 -96
  313. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +0 -59
  314. endoreg_db/data/requirement/event_cardiology.yaml +0 -251
  315. endoreg_db/data/requirement/event_requirements.yaml +0 -145
  316. endoreg_db/data/requirement/finding_colon_polyp.yaml +0 -50
  317. endoreg_db/data/requirement/gender.yaml +0 -25
  318. endoreg_db/data/requirement/lab_value.yaml +0 -441
  319. endoreg_db/data/requirement/medication.yaml +0 -93
  320. endoreg_db/data/requirement_operator/age.yaml +0 -13
  321. endoreg_db/data/requirement_operator/lab_operators.yaml +0 -129
  322. endoreg_db/data/requirement_operator/model_operators.yaml +0 -96
  323. endoreg_db/management/commands/init_default_ai_model.py +0 -112
  324. endoreg_db/management/commands/reset_celery_schedule.py +0 -9
  325. endoreg_db/management/commands/validate_video.py +0 -204
  326. endoreg_db/migrations/0002_requirementset_depends_on.py +0 -18
  327. endoreg_db/migrations/_old/0001_initial.py +0 -1857
  328. endoreg_db/migrations/_old/0002_add_video_correction_models.py +0 -52
  329. endoreg_db/migrations/_old/0003_add_center_display_name.py +0 -30
  330. endoreg_db/migrations/_old/0004_employee_city_employee_post_code_employee_street_and_more.py +0 -68
  331. endoreg_db/migrations/_old/0004_remove_casetemplate_rules_and_more.py +0 -77
  332. endoreg_db/migrations/_old/0005_merge_20251111_1003.py +0 -14
  333. endoreg_db/migrations/_old/0006_sensitivemeta_anonymized_text_and_more.py +0 -68
  334. endoreg_db/migrations/_old/0007_remove_rule_attribute_dtype_remove_rule_rule_type_and_more.py +0 -89
  335. endoreg_db/migrations/_old/0008_remove_event_event_classification_and_more.py +0 -27
  336. endoreg_db/migrations/_old/0009_alter_modelmeta_options_and_more.py +0 -21
  337. endoreg_db/renames.yml +0 -8
  338. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +0 -223
  339. endoreg_db/serializers/_old/raw_video_meta_validation.py +0 -179
  340. endoreg_db/serializers/_old/video.py +0 -71
  341. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +0 -115
  342. endoreg_db/serializers/meta/report_meta.py +0 -53
  343. endoreg_db/serializers/report/__init__.py +0 -9
  344. endoreg_db/serializers/report/mixins.py +0 -45
  345. endoreg_db/serializers/report/report.py +0 -105
  346. endoreg_db/serializers/report/report_list.py +0 -22
  347. endoreg_db/serializers/report/secure_file_url.py +0 -26
  348. endoreg_db/services/requirements_object.py +0 -147
  349. endoreg_db/services/storage_aware_video_processor.py +0 -370
  350. endoreg_db/urls/files.py +0 -6
  351. endoreg_db/urls/label_video_segment_validate.py +0 -33
  352. endoreg_db/urls/label_video_segments.py +0 -46
  353. endoreg_db/views/label/__init__.py +0 -5
  354. endoreg_db/views/label/label.py +0 -15
  355. endoreg_db/views/label_video_segment/__init__.py +0 -16
  356. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +0 -44
  357. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +0 -50
  358. endoreg_db/views/label_video_segment/label_video_segment.py +0 -77
  359. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +0 -174
  360. endoreg_db/views/label_video_segment/label_video_segment_detail.py +0 -73
  361. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +0 -46
  362. endoreg_db/views/label_video_segment/validate.py +0 -226
  363. endoreg_db/views/media/segments.py +0 -71
  364. endoreg_db/views/meta/available_files_list.py +0 -146
  365. endoreg_db/views/meta/report_meta.py +0 -53
  366. endoreg_db/views/meta/sensitive_meta_detail.py +0 -85
  367. endoreg_db/views/misc/secure_file_serving_view.py +0 -80
  368. endoreg_db/views/misc/secure_file_url_view.py +0 -84
  369. endoreg_db/views/misc/secure_url_validate.py +0 -79
  370. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +0 -164
  371. endoreg_db/views/patient_finding_location/__init__.py +0 -5
  372. endoreg_db/views/patient_finding_location/pfl_create.py +0 -70
  373. endoreg_db/views/patient_finding_morphology/__init__.py +0 -5
  374. endoreg_db/views/patient_finding_morphology/pfm_create.py +0 -70
  375. endoreg_db/views/pdf/__init__.py +0 -8
  376. endoreg_db/views/video/segmentation.py +0 -274
  377. endoreg_db/views/video/task_status.py +0 -49
  378. endoreg_db/views/video/timeline.py +0 -46
  379. endoreg_db/views/video/video_analyze.py +0 -52
  380. /endoreg_db/data/requirement/{colon_polyp_intervention.yaml → old/colon_polyp_intervention.yaml} +0 -0
  381. /endoreg_db/data/{_examples/requirement → requirement/old}/colonoscopy_baseline_austria.yaml +0 -0
  382. /endoreg_db/data/requirement/{coloreg_colon_polyp.yaml → old/coloreg_colon_polyp.yaml} +0 -0
  383. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_cardiovascular.yaml +0 -0
  384. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_classification_choice_cardiovascular.yaml +0 -0
  385. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_hepatology.yaml +0 -0
  386. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_misc.yaml +0 -0
  387. /endoreg_db/data/{_examples/requirement → requirement/old}/disease_renal.yaml +0 -0
  388. /endoreg_db/data/{_examples/requirement → requirement/old}/endoscopy_bleeding_risk.yaml +0 -0
  389. /endoreg_db/data/{_examples/requirement → requirement/old}/event_cardiology.yaml +0 -0
  390. /endoreg_db/data/{_examples/requirement → requirement/old}/event_requirements.yaml +0 -0
  391. /endoreg_db/data/{_examples/requirement → requirement/old}/finding_colon_polyp.yaml +0 -0
  392. /endoreg_db/{migrations/__init__.py → data/requirement/old/gender.yaml} +0 -0
  393. /endoreg_db/data/{_examples/requirement → requirement/old}/lab_value.yaml +0 -0
  394. /endoreg_db/data/{_examples/requirement → requirement/old}/medication.yaml +0 -0
  395. /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/age.yaml +0 -0
  396. /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/lab_operators.yaml +0 -0
  397. /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/model_operators.yaml +0 -0
  398. /endoreg_db/{urls/sensitive_meta.py → import_files/pseudonymization/__init__.py} +0 -0
  399. /endoreg_db/{views/pdf/pdf_stream_views.py → import_files/pseudonymization/pseudonymize.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-0.8.8.9.dist-info}/licenses/LICENSE +0 -0
@@ -1,128 +1,100 @@
1
1
  from django.core.management.base import BaseCommand
2
- from endoreg_db.models import (
3
- Finding, FindingType, Examination,
4
- FindingClassification, FindingClassificationType, FindingClassificationChoice,
5
- Organ,
6
- FindingIntervention, FindingInterventionType, LabValue, Contraindication
7
2
 
3
+ from endoreg_db.models import (
4
+ Finding,
5
+ FindingClassification,
6
+ FindingClassificationChoice,
7
+ FindingClassificationType,
8
+ FindingIntervention,
9
+ FindingInterventionType,
10
+ FindingType,
8
11
  )
9
- from ...utils import load_model_data_from_yaml
12
+
10
13
  from ...data import (
11
- FINDING_DATA_DIR, FINDING_TYPE_DATA_DIR,
14
+ FINDING_CLASSIFICATION_CHOICE_DATA_DIR,
15
+ FINDING_CLASSIFICATION_DATA_DIR,
16
+ FINDING_CLASSIFICATION_TYPE_DATA_DIR,
17
+ FINDING_DATA_DIR,
12
18
  FINDING_INTERVETION_DATA_DIR,
19
+ FINDING_TYPE_DATA_DIR,
13
20
  FINIDNG_INTERVENTION_TYPE_DATA_DIR,
14
- FINDING_CLASSIFICATION_TYPE_DATA_DIR,
15
- FINDING_CLASSIFICATION_DATA_DIR,
16
- FINDING_CLASSIFICATION_CHOICE_DATA_DIR
17
21
  )
22
+ from ...utils import load_model_data_from_yaml
18
23
 
19
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
24
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
20
25
  FindingInterventionType.__name__,
21
26
  FindingIntervention.__name__,
22
27
  FindingType.__name__,
23
- Finding.__name__,
24
- FindingClassificationType.__name__,
25
28
  FindingClassificationChoice.__name__,
29
+ FindingClassificationType.__name__,
26
30
  FindingClassification.__name__,
31
+ Finding.__name__,
27
32
  ]
28
33
 
29
34
  IMPORT_METADATA = {
30
35
  FindingType.__name__: {
31
- "dir": FINDING_TYPE_DATA_DIR, # e.g. "interventions"
32
- "model": FindingType, # e.g. Intervention
33
- "foreign_keys": [], # e.g. ["intervention_types"]
34
- "foreign_key_models": [] # e.g. [InterventionType]
36
+ "dir": FINDING_TYPE_DATA_DIR,
37
+ "model": FindingType,
38
+ "foreign_keys": [],
39
+ "foreign_key_models": [],
35
40
  },
36
41
  Finding.__name__: {
37
- "dir": FINDING_DATA_DIR, # e.g. "interventions"
38
- "model": Finding, # e.g. Intervention
39
- "foreign_keys": [
40
- "finding_types",
41
- "examinations",
42
- "finding_interventions",
43
- ], # e.g. ["intervention_types"]
44
- "foreign_key_models": [
45
- FindingType,
46
- Examination,
47
- FindingIntervention,
48
- FindingIntervention,
49
- FindingIntervention,
50
- ] # e.g. [InterventionType]
42
+ "dir": FINDING_DATA_DIR,
43
+ "model": Finding,
44
+ "foreign_keys": ["finding_types", "finding_interventions", "finding_classifications", "caused_by_interventions"],
45
+ "foreign_key_models": [FindingType, FindingIntervention, FindingClassification, FindingIntervention],
51
46
  },
52
47
  FindingInterventionType.__name__: {
53
- "dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR, # e.g. "interventions"
54
- "model": FindingInterventionType, # e.g. Intervention
55
- "foreign_keys": [], # e.g. ["intervention_types"]
56
- "foreign_key_models": [] # e.g. [InterventionType]
48
+ "dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR,
49
+ "model": FindingInterventionType,
50
+ "foreign_keys": [],
51
+ "foreign_key_models": [],
57
52
  },
58
53
  FindingIntervention.__name__: {
59
- "dir": FINDING_INTERVETION_DATA_DIR, # e.g. "interventions"
60
- "model": FindingIntervention, # e.g. Intervention
61
- "foreign_keys": [
62
- "intervention_types",
63
- "required_lab_values",
64
- "contraindications"
65
- ], # e.g. ["intervention_types"]
66
- "foreign_key_models": [
67
- FindingInterventionType,
68
- LabValue,
69
- Contraindication
70
- ] # e.g. [InterventionType]
54
+ "dir": FINDING_INTERVETION_DATA_DIR,
55
+ "model": FindingIntervention,
56
+ "foreign_keys": ["intervention_types"],
57
+ "foreign_key_models": [FindingInterventionType],
71
58
  },
72
59
  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]
60
+ "dir": FINDING_CLASSIFICATION_TYPE_DATA_DIR,
61
+ "model": FindingClassificationType,
62
+ "foreign_keys": [],
63
+ "foreign_key_models": [],
77
64
  },
78
65
  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"]
66
+ "dir": FINDING_CLASSIFICATION_DATA_DIR,
67
+ "model": FindingClassification,
68
+ "foreign_keys": ["classification_types", "findings", "finding_types", "choices"],
88
69
  "foreign_key_models": [
89
70
  FindingClassificationType,
90
71
  Finding,
91
- Examination,
92
72
  FindingType,
93
73
  FindingClassificationChoice,
94
- ] # e.g. [InterventionType]
74
+ ],
95
75
  },
96
76
  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]
77
+ "dir": FINDING_CLASSIFICATION_CHOICE_DATA_DIR,
78
+ "model": FindingClassificationChoice,
79
+ "foreign_keys": [],
80
+ "foreign_key_models": [],
105
81
  },
106
82
  }
107
83
 
84
+
108
85
  class Command(BaseCommand):
109
86
  help = """Load all .yaml files in the data/intervention directory
110
87
  into the Intervention and InterventionType model"""
111
88
 
112
89
  def add_arguments(self, parser):
113
90
  parser.add_argument(
114
- '--verbose',
115
- action='store_true',
116
- help='Display verbose output',
91
+ "--verbose",
92
+ action="store_true",
93
+ help="Display verbose output",
117
94
  )
118
95
 
119
96
  def handle(self, *args, **options):
120
- verbose = options['verbose']
97
+ verbose = options["verbose"]
121
98
  for model_name in IMPORT_MODELS:
122
99
  _metadata = IMPORT_METADATA[model_name]
123
- load_model_data_from_yaml(
124
- self,
125
- model_name,
126
- _metadata,
127
- verbose
128
- )
100
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -1,51 +1,49 @@
1
- from django.conf import settings
2
1
  import os
2
+
3
+ from django.conf import settings
3
4
  from django.core.management.base import BaseCommand
5
+
6
+ from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
4
7
  from ...models import InformationSource, InformationSourceType
5
8
  from ...utils import load_model_data_from_yaml
6
- from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
7
9
 
8
- SOURCE_DIR = INFORMATION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
10
+ SOURCE_DIR = INFORMATION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
9
11
 
10
12
 
11
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
13
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
14
  InformationSourceType.__name__,
13
15
  InformationSource.__name__,
14
16
  ]
15
17
 
16
18
  IMPORT_METADATA = {
17
19
  InformationSourceType.__name__: {
18
- "dir": INFORMATION_SOURCE_TYPE_DATA_DIR, # e.g. "intervention_type"
19
- "model": InformationSourceType, # e.g. InterventionType
20
- "foreign_keys": [], # e.g. ["intervention_types"]
21
- "foreign_key_models": [] # e.g. [InterventionType]
20
+ "dir": INFORMATION_SOURCE_TYPE_DATA_DIR, # e.g. "intervention_type"
21
+ "model": InformationSourceType,
22
+ "foreign_keys": [], # e.g. ["intervention_types"]
23
+ "foreign_key_models": [], # e.g. [InterventionType]
22
24
  },
23
25
  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]
28
- }
26
+ "dir": SOURCE_DIR, # e.g. "interventions"
27
+ "model": InformationSource,
28
+ "foreign_keys": ["information_source_types"], # e.g. ["intervention_types"]
29
+ "foreign_key_models": [InformationSourceType], # e.g. [InterventionType]
30
+ },
29
31
  }
30
32
 
33
+
31
34
  class Command(BaseCommand):
32
35
  help = """Load all .yaml files in the data/intervention directory
33
36
  into the Intervention and InterventionType model"""
34
37
 
35
38
  def add_arguments(self, parser):
36
39
  parser.add_argument(
37
- '--verbose',
38
- action='store_true',
39
- help='Display verbose output',
40
+ "--verbose",
41
+ action="store_true",
42
+ help="Display verbose output",
40
43
  )
41
44
 
42
45
  def handle(self, *args, **options):
43
- verbose = options['verbose']
46
+ verbose = options["verbose"]
44
47
  for model_name in IMPORT_MODELS:
45
48
  _metadata = IMPORT_METADATA[model_name]
46
- load_model_data_from_yaml(
47
- self,
48
- model_name,
49
- _metadata,
50
- verbose
51
- )
49
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -1,50 +1,41 @@
1
1
  from django.core.management.base import BaseCommand
2
+
2
3
  from endoreg_db.models import LabValue as MODEL_0
3
- from endoreg_db.models import PatientLabSampleType, NumericValueDistribution
4
- from ...utils import load_model_data_from_yaml
4
+ from endoreg_db.models import NumericValueDistribution, PatientLabSampleType, Unit
5
+
5
6
  from ...data import LAB_VALUE_DATA_DIR as SOURCE_DIR
6
7
  from ...data import PATIENT_LAB_SAMPLE_TYPE_DATA_DIR
8
+ from ...utils import load_model_data_from_yaml
7
9
 
8
- from endoreg_db.models import Unit
9
-
10
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
10
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
11
11
  MODEL_0.__name__,
12
- PatientLabSampleType.__name__
12
+ PatientLabSampleType.__name__,
13
13
  ]
14
14
 
15
15
  IMPORT_METADATA = {
16
16
  MODEL_0.__name__: {
17
- "dir": SOURCE_DIR, # e.g. "interventions"
18
- "model": MODEL_0, # e.g. Intervention
19
- "foreign_keys": ["default_unit","default_numerical_value_distribution"], # e.g. ["intervention_types"]
20
- "foreign_key_models": [Unit, NumericValueDistribution] # e.g. [InterventionType]
17
+ "dir": SOURCE_DIR, # e.g. "interventions"
18
+ "model": MODEL_0,
19
+ "foreign_keys": ["default_unit", "default_numerical_value_distribution"], # e.g. ["intervention_types"]
20
+ "foreign_key_models": [Unit, NumericValueDistribution], # e.g. [InterventionType]
21
21
  },
22
- PatientLabSampleType.__name__: {
23
- "dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR,
24
- "model": PatientLabSampleType,
25
- "foreign_keys": [],
26
- "foreign_key_models": []
27
- }
22
+ PatientLabSampleType.__name__: {"dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR, "model": PatientLabSampleType, "foreign_keys": [], "foreign_key_models": []},
28
23
  }
29
24
 
25
+
30
26
  class Command(BaseCommand):
31
27
  help = """Load all .yaml files in the data/intervention directory
32
28
  into the Intervention and InterventionType model"""
33
29
 
34
30
  def add_arguments(self, parser):
35
31
  parser.add_argument(
36
- '--verbose',
37
- action='store_true',
38
- help='Display verbose output',
32
+ "--verbose",
33
+ action="store_true",
34
+ help="Display verbose output",
39
35
  )
40
36
 
41
37
  def handle(self, *args, **options):
42
- verbose = options['verbose']
38
+ verbose = options["verbose"]
43
39
  for model_name in IMPORT_MODELS:
44
40
  _metadata = IMPORT_METADATA[model_name]
45
- load_model_data_from_yaml(
46
- self,
47
- model_name,
48
- _metadata,
49
- verbose
50
- )
41
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -1,25 +1,26 @@
1
1
  from django.core.management.base import BaseCommand
2
+
2
3
  from endoreg_db.models import (
4
+ Disease,
5
+ DiseaseClassificationChoice,
6
+ Event,
7
+ InformationSource,
3
8
  Medication,
4
9
  MedicationIndication,
5
10
  MedicationIndicationType,
6
11
  MedicationIntakeTime,
7
12
  MedicationSchedule,
8
13
  Unit,
9
- Disease,
10
- Event,
11
- InformationSource,
12
- DiseaseClassificationChoice,
13
14
  )
14
- from ...utils import load_model_data_from_yaml
15
+
15
16
  from ...data import (
16
17
  MEDICATION_DATA_DIR,
18
+ MEDICATION_INDICATION_DATA_DIR,
17
19
  MEDICATION_INDICATION_TYPE_DATA_DIR,
18
20
  MEDICATION_INTAKE_TIME_DATA_DIR,
19
21
  MEDICATION_SCHEDULE_DATA_DIR,
20
- MEDICATION_INDICATION_DATA_DIR,
21
22
  )
22
-
23
+ from ...utils import load_model_data_from_yaml
23
24
 
24
25
  IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
25
26
  Medication.__name__,
@@ -32,25 +33,25 @@ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
32
33
  IMPORT_METADATA = {
33
34
  Medication.__name__: {
34
35
  "dir": MEDICATION_DATA_DIR, # e.g. "interventions"
35
- "model": Medication, # e.g. Intervention
36
+ "model": Medication,
36
37
  "foreign_keys": ["default_unit"], # e.g. ["intervention_types"]
37
38
  "foreign_key_models": [Unit], # e.g. [InterventionType]
38
39
  },
39
40
  MedicationIndicationType.__name__: {
40
41
  "dir": MEDICATION_INDICATION_TYPE_DATA_DIR, # e.g. "interventions"
41
- "model": MedicationIndicationType, # e.g. Intervention
42
+ "model": MedicationIndicationType,
42
43
  "foreign_keys": [], # e.g. ["intervention_types"]
43
44
  "foreign_key_models": [], # e.g. [InterventionType]
44
45
  },
45
46
  MedicationIntakeTime.__name__: {
46
47
  "dir": MEDICATION_INTAKE_TIME_DATA_DIR, # e.g. "interventions"
47
- "model": MedicationIntakeTime, # e.g. Intervention
48
+ "model": MedicationIntakeTime,
48
49
  "foreign_keys": [], # e.g. ["intervention_types"]
49
50
  "foreign_key_models": [], # e.g. [InterventionType]
50
51
  },
51
52
  MedicationSchedule.__name__: {
52
53
  "dir": MEDICATION_SCHEDULE_DATA_DIR, # e.g. "interventions"
53
- "model": MedicationSchedule, # e.g. Intervention
54
+ "model": MedicationSchedule,
54
55
  "foreign_keys": [
55
56
  "medication",
56
57
  "intake_times",
@@ -64,7 +65,7 @@ IMPORT_METADATA = {
64
65
  },
65
66
  MedicationIndication.__name__: {
66
67
  "dir": MEDICATION_INDICATION_DATA_DIR, # e.g. "interventions"
67
- "model": MedicationIndication, # e.g. Intervention
68
+ "model": MedicationIndication,
68
69
  "foreign_keys": [
69
70
  "indication_type",
70
71
  "medication_schedules",
@@ -1,43 +1,39 @@
1
1
  from django.core.management.base import BaseCommand
2
+
2
3
  from endoreg_db.models import Organ
4
+
5
+ from ...data import ORGAN_DATA_DIR
3
6
  from ...utils import load_model_data_from_yaml
4
- from ...data import (
5
- ORGAN_DATA_DIR
6
- )
7
7
 
8
8
  MODEL_0 = Organ
9
9
 
10
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
11
- MODEL_0.__name__,#
10
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
11
+ MODEL_0.__name__, #
12
12
  ]
13
13
 
14
14
  IMPORT_METADATA = {
15
15
  MODEL_0.__name__: {
16
- "dir": ORGAN_DATA_DIR, # e.g. "interventions"
17
- "model": MODEL_0, # e.g. Intervention
18
- "foreign_keys": [], # e.g. ["intervention_types"]
19
- "foreign_key_models": [] # e.g. [InterventionType]
16
+ "dir": ORGAN_DATA_DIR, # e.g. "interventions"
17
+ "model": MODEL_0,
18
+ "foreign_keys": [], # e.g. ["intervention_types"]
19
+ "foreign_key_models": [], # e.g. [InterventionType]
20
20
  }
21
21
  }
22
22
 
23
+
23
24
  class Command(BaseCommand):
24
25
  help = """Load all .yaml files in the data/intervention directory
25
26
  into the Intervention and InterventionType model"""
26
27
 
27
28
  def add_arguments(self, parser):
28
29
  parser.add_argument(
29
- '--verbose',
30
- action='store_true',
31
- help='Display verbose output',
30
+ "--verbose",
31
+ action="store_true",
32
+ help="Display verbose output",
32
33
  )
33
34
 
34
35
  def handle(self, *args, **options):
35
- verbose = options['verbose']
36
+ verbose = options["verbose"]
36
37
  for model_name in IMPORT_MODELS:
37
38
  _metadata = IMPORT_METADATA[model_name]
38
- load_model_data_from_yaml(
39
- self,
40
- model_name,
41
- _metadata,
42
- verbose
43
- )
39
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -1,27 +1,29 @@
1
- from django.conf import settings
2
1
  import os
3
- from django.core.management.base import BaseCommand
4
2
 
5
3
  import yaml
6
- from ...utils import load_model_data_from_yaml
4
+ from django.conf import settings
5
+ from django.core.management.base import BaseCommand
7
6
 
7
+ from ...data import REPORT_TYPE_DATA_DIR
8
8
 
9
9
  #### CUSTOMIZE
10
10
  from ...models import PdfType, ReportReaderFlag
11
- from ...data import PDF_TYPE_DATA_DIR
11
+ from ...utils import load_model_data_from_yaml
12
12
 
13
- SOURCE_DIR = PDF_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
13
+ SOURCE_DIR = REPORT_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
14
14
 
15
15
  MODEL_0 = PdfType
16
16
 
17
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
17
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
18
18
  MODEL_0.__name__,
19
19
  ]
20
20
 
21
21
  IMPORT_METADATA = {
22
22
  MODEL_0.__name__: {
23
- "dir": SOURCE_DIR, # e.g. "interventions"
24
- "model": MODEL_0, # e.g. Intervention
23
+ "dir": SOURCE_DIR, # e.g. "interventions"
24
+ "model": MODEL_0, # e.g. Intervention
25
+ "dir": SOURCE_DIR, # e.g. "interventions"
26
+ "model": MODEL_0,
25
27
  "foreign_keys": [
26
28
  "patient_info_line",
27
29
  "endoscope_info_line",
@@ -39,23 +41,22 @@ IMPORT_METADATA = {
39
41
  }
40
42
  }
41
43
 
44
+
42
45
  class Command(BaseCommand):
43
46
  help = f"""Load all .yaml files in the {SOURCE_DIR} directory"""
44
47
 
45
48
  def add_arguments(self, parser):
46
49
  parser.add_argument(
47
- '--verbose',
48
- action='store_true',
49
- help='Display verbose output',
50
+ "--verbose",
51
+ action="store_true",
52
+ help="Display verbose output",
50
53
  )
51
54
 
52
55
  def handle(self, *args, **options):
53
- verbose = options['verbose']
56
+ verbose = options["verbose"]
57
+ verbose = options["verbose"]
54
58
  for model_name in IMPORT_MODELS:
55
59
  _metadata = IMPORT_METADATA[model_name]
56
- load_model_data_from_yaml(
57
- self,
58
- model_name,
59
- _metadata,
60
- verbose
61
- )
60
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
61
+
62
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -1,44 +1,41 @@
1
1
  from django.conf import settings
2
2
  from django.core.management.base import BaseCommand
3
+
4
+ from ...data import PROFESSION_DATA_DIR
3
5
  from ...models import Profession
4
6
  from ...utils import load_model_data_from_yaml
5
- from ...data import PROFESSION_DATA_DIR
6
7
 
7
- SOURCE_DIR = PROFESSION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
8
+ SOURCE_DIR = PROFESSION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
8
9
 
9
10
  MODEL_0 = Profession
10
11
 
11
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
13
  MODEL_0.__name__,
13
14
  ]
14
15
 
15
16
  IMPORT_METADATA = {
16
17
  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]
18
+ "dir": SOURCE_DIR, # e.g. "interventions"
19
+ "model": MODEL_0,
20
+ "foreign_keys": [], # e.g. ["intervention_types"]
21
+ "foreign_key_models": [], # e.g. [InterventionType]
21
22
  }
22
23
  }
23
24
 
25
+
24
26
  class Command(BaseCommand):
25
27
  help = """Load all .yaml files in the data/intervention directory
26
28
  into the Intervention and InterventionType model"""
27
29
 
28
30
  def add_arguments(self, parser):
29
31
  parser.add_argument(
30
- '--verbose',
31
- action='store_true',
32
- help='Display verbose output',
32
+ "--verbose",
33
+ action="store_true",
34
+ help="Display verbose output",
33
35
  )
34
36
 
35
37
  def handle(self, *args, **options):
36
- verbose = options['verbose']
38
+ verbose = options["verbose"]
37
39
  for model_name in IMPORT_MODELS:
38
40
  _metadata = IMPORT_METADATA[model_name]
39
- load_model_data_from_yaml(
40
- self,
41
- model_name,
42
- _metadata,
43
- verbose
44
- )
41
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -1,33 +1,35 @@
1
1
  from django.core.management.base import BaseCommand
2
+
3
+ from ...data import QUALIFICATION_DATA_DIR
2
4
  from ...models import Qualification, QualificationType
3
5
  from ...utils import load_model_data_from_yaml
4
- from ...data import QUALIFICATION_DATA_DIR
5
6
 
6
- SOURCE_DIR = QUALIFICATION_DATA_DIR # qualification data directory
7
+ SOURCE_DIR = QUALIFICATION_DATA_DIR # qualification data directory
7
8
 
8
9
  model_0 = QualificationType
9
10
  model_1 = Qualification
10
11
 
11
- IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
12
13
  model_0.__name__,
13
14
  model_1.__name__,
14
15
  ]
15
16
 
16
17
  IMPORT_METADATA = {
17
18
  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]
19
+ "dir": SOURCE_DIR, # e.g. "interventions"
20
+ "model": model_0,
21
+ "foreign_keys": [], # e.g. ["intervention_types"]
22
+ "foreign_key_models": [], # e.g. [InterventionType]
22
23
  },
23
24
  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
- }
25
+ "dir": SOURCE_DIR, # e.g. "interventions"
26
+ "model": model_1,
27
+ "foreign_keys": ["qualification_types"], # e.g. ["intervention_types"]
28
+ "foreign_key_models": [model_0], # e.g. [InterventionType]
29
+ },
29
30
  }
30
31
 
32
+
31
33
  class Command(BaseCommand):
32
34
  help = """Load all .yaml files in the data/qualification directory
33
35
  into the Qualification / Qualification Type model"""
@@ -37,23 +39,18 @@ class Command(BaseCommand):
37
39
  Adds the --verbose flag to the command-line parser to enable detailed output.
38
40
  """
39
41
  parser.add_argument(
40
- '--verbose',
41
- action='store_true',
42
- help='Display verbose output',
42
+ "--verbose",
43
+ action="store_true",
44
+ help="Display verbose output",
43
45
  )
44
46
 
45
47
  def handle(self, *args, **options):
46
48
  """
47
49
  Loads data from YAML files into the QualificationType and Qualification models.
48
-
50
+
49
51
  Iterates over predefined models and imports their data from YAML files using associated metadata. Supports verbose output if enabled via command-line options.
50
52
  """
51
- verbose = options['verbose']
53
+ verbose = options["verbose"]
52
54
  for model_name in IMPORT_MODELS:
53
55
  _metadata = IMPORT_METADATA[model_name]
54
- load_model_data_from_yaml(
55
- self,
56
- model_name,
57
- _metadata,
58
- verbose
59
- )
56
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)