endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

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  1. endoreg_db/case_generator/__init__.py +0 -0
  2. endoreg_db/case_generator/case_generator.py +159 -0
  3. endoreg_db/case_generator/lab_sample_factory.py +33 -0
  4. endoreg_db/case_generator/utils.py +30 -0
  5. endoreg_db/data/__init__.py +118 -0
  6. endoreg_db/data/agl_service/data.yaml +19 -0
  7. endoreg_db/data/ai_model/data.yaml +7 -0
  8. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  9. endoreg_db/data/ai_model_label/label-set/data.yaml +21 -0
  10. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  11. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +5 -0
  12. endoreg_db/data/ai_model_type/data.yaml +7 -0
  13. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  14. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  15. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  16. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  17. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  18. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  19. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  20. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  21. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  22. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  23. endoreg_db/data/case_template/rule_value/.init +0 -0
  24. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  25. endoreg_db/data/case_template/template/base.yaml +8 -0
  26. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  27. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  28. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  29. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  30. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  31. endoreg_db/data/center/data.yaml +90 -0
  32. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  33. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  34. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  35. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  36. endoreg_db/data/disease/hepatology.yaml +5 -0
  37. endoreg_db/data/disease/misc.yaml +6 -0
  38. endoreg_db/data/disease/renal.yaml +5 -0
  39. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  40. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  41. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  42. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  43. endoreg_db/data/distribution/date/patient.yaml +7 -0
  44. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  45. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  46. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  47. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  48. endoreg_db/data/endoscope/data.yaml +93 -0
  49. endoreg_db/data/endoscope_type/data.yaml +11 -0
  50. endoreg_db/data/endoscopy_processor/data.yaml +47 -0
  51. endoreg_db/data/event/cardiology.yaml +28 -0
  52. endoreg_db/data/event/neurology.yaml +14 -0
  53. endoreg_db/data/event/surgery.yaml +13 -0
  54. endoreg_db/data/event/thrombembolism.yaml +20 -0
  55. endoreg_db/data/examination/examinations/data.yaml +66 -0
  56. endoreg_db/data/examination/time/data.yaml +48 -0
  57. endoreg_db/data/examination/time-type/data.yaml +8 -0
  58. endoreg_db/data/examination/type/data.yaml +5 -0
  59. endoreg_db/data/examination_indication/endoscopy.yaml +8 -0
  60. endoreg_db/data/examination_indication_classification/endoscopy.yaml +8 -0
  61. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  62. endoreg_db/data/finding/data.yaml +141 -0
  63. endoreg_db/data/finding_intervention/endoscopy.yaml +138 -0
  64. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  65. endoreg_db/data/finding_location_classification/colonoscopy.yaml +46 -0
  66. endoreg_db/data/finding_location_classification_choice/colonoscopy.yaml +240 -0
  67. endoreg_db/data/finding_morphology_classification/colonoscopy.yaml +48 -0
  68. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_circularity_default.yaml +34 -0
  69. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_nice.yaml +20 -0
  70. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_paris.yaml +65 -0
  71. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_planarity_default.yaml +56 -0
  72. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_surface_intact_default.yaml +39 -0
  73. endoreg_db/data/finding_morphology_classification_choice/colonoscopy_size.yaml +57 -0
  74. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  75. endoreg_db/data/finding_type/data.yaml +30 -0
  76. endoreg_db/data/gender/data.yaml +35 -0
  77. endoreg_db/data/information_source/data.yaml +30 -0
  78. endoreg_db/data/information_source/medication.yaml +6 -0
  79. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  80. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  81. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  82. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  83. endoreg_db/data/lab_value/hematology.yaml +184 -0
  84. endoreg_db/data/lab_value/hormones.yaml +59 -0
  85. endoreg_db/data/lab_value/lipids.yaml +53 -0
  86. endoreg_db/data/lab_value/misc.yaml +33 -0
  87. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  88. endoreg_db/data/log_type/data.yaml +57 -0
  89. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  90. endoreg_db/data/lx_client_type/base.yaml +30 -0
  91. endoreg_db/data/lx_permission/base.yaml +24 -0
  92. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  93. endoreg_db/data/material/material.yaml +91 -0
  94. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  95. endoreg_db/data/medication/tah.yaml +70 -0
  96. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  97. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  98. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  99. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  100. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  101. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  102. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  103. endoreg_db/data/names_first/first_names.yaml +51 -0
  104. endoreg_db/data/names_last/last_names.yaml +51 -0
  105. endoreg_db/data/network_device/data.yaml +59 -0
  106. endoreg_db/data/network_device_type/data.yaml +12 -0
  107. endoreg_db/data/organ/data.yaml +29 -0
  108. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  109. endoreg_db/data/pdf_type/data.yaml +29 -0
  110. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  111. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  112. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  113. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  114. endoreg_db/data/profession/data.yaml +70 -0
  115. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  116. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  117. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +19 -0
  118. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  119. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  120. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  121. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  122. endoreg_db/data/unit/concentration.yaml +92 -0
  123. endoreg_db/data/unit/data.yaml +17 -0
  124. endoreg_db/data/unit/length.yaml +31 -0
  125. endoreg_db/data/unit/misc.yaml +20 -0
  126. endoreg_db/data/unit/rate.yaml +6 -0
  127. endoreg_db/data/unit/time.yaml +13 -0
  128. endoreg_db/data/unit/volume.yaml +35 -0
  129. endoreg_db/data/unit/weight.yaml +38 -0
  130. endoreg_db/data/waste/data.yaml +12 -0
  131. endoreg_db/forms/__init__.py +5 -0
  132. endoreg_db/forms/examination_form.py +11 -0
  133. endoreg_db/forms/patient_finding_intervention_form.py +19 -0
  134. endoreg_db/forms/patient_form.py +26 -0
  135. endoreg_db/forms/questionnaires/__init__.py +1 -0
  136. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  137. endoreg_db/forms/settings/__init__.py +8 -0
  138. endoreg_db/forms/unit.py +6 -0
  139. endoreg_db/management/__init__.py +0 -0
  140. endoreg_db/management/commands/__init__.py +0 -0
  141. endoreg_db/management/commands/_load_model_template.py +41 -0
  142. endoreg_db/management/commands/delete_all.py +18 -0
  143. endoreg_db/management/commands/fetch_legacy_image_dataset.py +32 -0
  144. endoreg_db/management/commands/fix_auth_permission.py +20 -0
  145. endoreg_db/management/commands/load_active_model_data.py +45 -0
  146. endoreg_db/management/commands/load_ai_model_data.py +79 -0
  147. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  148. endoreg_db/management/commands/load_base_db_data.py +178 -0
  149. endoreg_db/management/commands/load_center_data.py +43 -0
  150. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  151. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  152. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  153. endoreg_db/management/commands/load_disease_data.py +62 -0
  154. endoreg_db/management/commands/load_distribution_data.py +66 -0
  155. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  156. endoreg_db/management/commands/load_event_data.py +41 -0
  157. endoreg_db/management/commands/load_examination_data.py +75 -0
  158. endoreg_db/management/commands/load_examination_indication_data.py +65 -0
  159. endoreg_db/management/commands/load_finding_data.py +171 -0
  160. endoreg_db/management/commands/load_g_play_data.py +113 -0
  161. endoreg_db/management/commands/load_gender_data.py +44 -0
  162. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +133 -0
  163. endoreg_db/management/commands/load_information_source.py +45 -0
  164. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  165. endoreg_db/management/commands/load_logging_data.py +39 -0
  166. endoreg_db/management/commands/load_lx_data.py +64 -0
  167. endoreg_db/management/commands/load_medication_data.py +103 -0
  168. endoreg_db/management/commands/load_medication_indication_data.py +63 -0
  169. endoreg_db/management/commands/load_medication_indication_type_data.py +41 -0
  170. endoreg_db/management/commands/load_medication_intake_time_data.py +41 -0
  171. endoreg_db/management/commands/load_medication_schedule_data.py +55 -0
  172. endoreg_db/management/commands/load_name_data.py +37 -0
  173. endoreg_db/management/commands/load_network_data.py +57 -0
  174. endoreg_db/management/commands/load_organ_data.py +43 -0
  175. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  176. endoreg_db/management/commands/load_profession_data.py +44 -0
  177. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  178. endoreg_db/management/commands/load_unit_data.py +46 -0
  179. endoreg_db/management/commands/load_user_groups.py +28 -0
  180. endoreg_db/management/commands/register_ai_model.py +64 -0
  181. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  182. endoreg_db/migrations/0001_initial.py +2045 -0
  183. endoreg_db/migrations/0002_alter_frame_image_alter_rawframe_image.py +23 -0
  184. endoreg_db/migrations/0003_alter_frame_image_alter_rawframe_image.py +23 -0
  185. endoreg_db/migrations/0004_alter_rawvideofile_file_alter_video_file.py +25 -0
  186. endoreg_db/migrations/0005_rawvideofile_frame_count_and_more.py +33 -0
  187. endoreg_db/migrations/0006_frame_extracted_rawframe_extracted.py +23 -0
  188. endoreg_db/migrations/0007_rename_pseudo_patient_video_patient_and_more.py +24 -0
  189. endoreg_db/migrations/0008_remove_reportfile_patient_examination_and_more.py +48 -0
  190. endoreg_db/migrations/__init__.py +0 -0
  191. endoreg_db/models/__init__.py +376 -0
  192. endoreg_db/models/ai_model/__init__.py +4 -0
  193. endoreg_db/models/ai_model/active_model.py +9 -0
  194. endoreg_db/models/ai_model/ai_model.py +103 -0
  195. endoreg_db/models/ai_model/lightning/__init__.py +3 -0
  196. endoreg_db/models/ai_model/lightning/inference_dataset.py +53 -0
  197. endoreg_db/models/ai_model/lightning/multilabel_classification_net.py +155 -0
  198. endoreg_db/models/ai_model/lightning/postprocess.py +53 -0
  199. endoreg_db/models/ai_model/lightning/predict.py +172 -0
  200. endoreg_db/models/ai_model/lightning/prediction_visualizer.py +55 -0
  201. endoreg_db/models/ai_model/lightning/preprocess.py +68 -0
  202. endoreg_db/models/ai_model/lightning/run_visualizer.py +21 -0
  203. endoreg_db/models/ai_model/model_meta.py +250 -0
  204. endoreg_db/models/ai_model/model_type.py +36 -0
  205. endoreg_db/models/ai_model/utils.py +8 -0
  206. endoreg_db/models/annotation/__init__.py +32 -0
  207. endoreg_db/models/annotation/anonymized_image_annotation.py +115 -0
  208. endoreg_db/models/annotation/binary_classification_annotation_task.py +117 -0
  209. endoreg_db/models/annotation/image_classification.py +86 -0
  210. endoreg_db/models/annotation/video_segmentation_annotation.py +52 -0
  211. endoreg_db/models/annotation/video_segmentation_labelset.py +20 -0
  212. endoreg_db/models/case/__init__.py +1 -0
  213. endoreg_db/models/case/case.py +34 -0
  214. endoreg_db/models/case_template/__init__.py +15 -0
  215. endoreg_db/models/case_template/case_template.py +125 -0
  216. endoreg_db/models/case_template/case_template_rule.py +276 -0
  217. endoreg_db/models/case_template/case_template_rule_value.py +88 -0
  218. endoreg_db/models/case_template/case_template_type.py +28 -0
  219. endoreg_db/models/center/__init__.py +11 -0
  220. endoreg_db/models/center/center.py +51 -0
  221. endoreg_db/models/center/center_product.py +33 -0
  222. endoreg_db/models/center/center_resource.py +33 -0
  223. endoreg_db/models/center/center_waste.py +16 -0
  224. endoreg_db/models/contraindication/__init__.py +21 -0
  225. endoreg_db/models/data_file/__init__.py +39 -0
  226. endoreg_db/models/data_file/base_classes/__init__.py +7 -0
  227. endoreg_db/models/data_file/base_classes/abstract_frame.py +100 -0
  228. endoreg_db/models/data_file/base_classes/abstract_pdf.py +136 -0
  229. endoreg_db/models/data_file/base_classes/abstract_video.py +807 -0
  230. endoreg_db/models/data_file/base_classes/frame_helpers.py +17 -0
  231. endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +19 -0
  232. endoreg_db/models/data_file/base_classes/utils.py +80 -0
  233. endoreg_db/models/data_file/frame.py +29 -0
  234. endoreg_db/models/data_file/import_classes/__init__.py +18 -0
  235. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +35 -0
  236. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +28 -0
  237. endoreg_db/models/data_file/import_classes/processing_functions/video.py +260 -0
  238. endoreg_db/models/data_file/import_classes/raw_pdf.py +260 -0
  239. endoreg_db/models/data_file/import_classes/raw_video.py +288 -0
  240. endoreg_db/models/data_file/metadata/__init__.py +13 -0
  241. endoreg_db/models/data_file/metadata/pdf_meta.py +74 -0
  242. endoreg_db/models/data_file/metadata/sensitive_meta.py +290 -0
  243. endoreg_db/models/data_file/metadata/video_meta.py +199 -0
  244. endoreg_db/models/data_file/report_file.py +56 -0
  245. endoreg_db/models/data_file/video/__init__.py +11 -0
  246. endoreg_db/models/data_file/video/import_meta.py +25 -0
  247. endoreg_db/models/data_file/video/video.py +196 -0
  248. endoreg_db/models/data_file/video_segment.py +214 -0
  249. endoreg_db/models/disease.py +79 -0
  250. endoreg_db/models/emission/__init__.py +5 -0
  251. endoreg_db/models/emission/emission_factor.py +85 -0
  252. endoreg_db/models/event.py +73 -0
  253. endoreg_db/models/examination/__init__.py +9 -0
  254. endoreg_db/models/examination/examination.py +67 -0
  255. endoreg_db/models/examination/examination_indication.py +170 -0
  256. endoreg_db/models/examination/examination_time.py +53 -0
  257. endoreg_db/models/examination/examination_time_type.py +48 -0
  258. endoreg_db/models/examination/examination_type.py +40 -0
  259. endoreg_db/models/finding/__init__.py +11 -0
  260. endoreg_db/models/finding/finding.py +75 -0
  261. endoreg_db/models/finding/finding_intervention.py +60 -0
  262. endoreg_db/models/finding/finding_location_classification.py +94 -0
  263. endoreg_db/models/finding/finding_morphology_classification.py +89 -0
  264. endoreg_db/models/finding/finding_type.py +22 -0
  265. endoreg_db/models/hardware/__init__.py +2 -0
  266. endoreg_db/models/hardware/endoscope.py +60 -0
  267. endoreg_db/models/hardware/endoscopy_processor.py +155 -0
  268. endoreg_db/models/information_source.py +29 -0
  269. endoreg_db/models/label/__init__.py +1 -0
  270. endoreg_db/models/label/label.py +112 -0
  271. endoreg_db/models/laboratory/__init__.py +1 -0
  272. endoreg_db/models/laboratory/lab_value.py +111 -0
  273. endoreg_db/models/logging/__init__.py +11 -0
  274. endoreg_db/models/logging/agl_service.py +19 -0
  275. endoreg_db/models/logging/base.py +22 -0
  276. endoreg_db/models/logging/log_type.py +23 -0
  277. endoreg_db/models/logging/network_device.py +27 -0
  278. endoreg_db/models/lx/__init__.py +4 -0
  279. endoreg_db/models/lx/client.py +57 -0
  280. endoreg_db/models/lx/identity.py +34 -0
  281. endoreg_db/models/lx/permission.py +18 -0
  282. endoreg_db/models/lx/user.py +16 -0
  283. endoreg_db/models/medication/__init__.py +19 -0
  284. endoreg_db/models/medication/medication.py +33 -0
  285. endoreg_db/models/medication/medication_indication.py +50 -0
  286. endoreg_db/models/medication/medication_indication_type.py +34 -0
  287. endoreg_db/models/medication/medication_intake_time.py +26 -0
  288. endoreg_db/models/medication/medication_schedule.py +37 -0
  289. endoreg_db/models/network/__init__.py +9 -0
  290. endoreg_db/models/network/agl_service.py +38 -0
  291. endoreg_db/models/network/network_device.py +58 -0
  292. endoreg_db/models/network/network_device_type.py +23 -0
  293. endoreg_db/models/organ/__init__.py +38 -0
  294. endoreg_db/models/other/__init__.py +23 -0
  295. endoreg_db/models/other/distribution/__init__.py +44 -0
  296. endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
  297. endoreg_db/models/other/distribution/date_value_distribution.py +91 -0
  298. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
  299. endoreg_db/models/other/distribution/numeric_value_distribution.py +97 -0
  300. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
  301. endoreg_db/models/other/distribution.py +5 -0
  302. endoreg_db/models/other/material.py +20 -0
  303. endoreg_db/models/other/resource.py +18 -0
  304. endoreg_db/models/other/transport_route.py +22 -0
  305. endoreg_db/models/other/waste.py +20 -0
  306. endoreg_db/models/patient/__init__.py +24 -0
  307. endoreg_db/models/patient/patient_examination.py +182 -0
  308. endoreg_db/models/patient/patient_finding.py +143 -0
  309. endoreg_db/models/patient/patient_finding_intervention.py +26 -0
  310. endoreg_db/models/patient/patient_finding_location.py +120 -0
  311. endoreg_db/models/patient/patient_finding_morphology.py +166 -0
  312. endoreg_db/models/permissions/__init__.py +44 -0
  313. endoreg_db/models/persons/__init__.py +34 -0
  314. endoreg_db/models/persons/examiner/__init__.py +2 -0
  315. endoreg_db/models/persons/examiner/examiner.py +60 -0
  316. endoreg_db/models/persons/examiner/examiner_type.py +2 -0
  317. endoreg_db/models/persons/first_name.py +18 -0
  318. endoreg_db/models/persons/gender.py +22 -0
  319. endoreg_db/models/persons/last_name.py +20 -0
  320. endoreg_db/models/persons/patient/__init__.py +8 -0
  321. endoreg_db/models/persons/patient/patient.py +389 -0
  322. endoreg_db/models/persons/patient/patient_disease.py +22 -0
  323. endoreg_db/models/persons/patient/patient_event.py +52 -0
  324. endoreg_db/models/persons/patient/patient_examination_indication.py +32 -0
  325. endoreg_db/models/persons/patient/patient_lab_sample.py +108 -0
  326. endoreg_db/models/persons/patient/patient_lab_value.py +197 -0
  327. endoreg_db/models/persons/patient/patient_medication.py +59 -0
  328. endoreg_db/models/persons/patient/patient_medication_schedule.py +88 -0
  329. endoreg_db/models/persons/person.py +31 -0
  330. endoreg_db/models/persons/portal_user_information.py +27 -0
  331. endoreg_db/models/prediction/__init__.py +8 -0
  332. endoreg_db/models/prediction/image_classification.py +51 -0
  333. endoreg_db/models/prediction/video_prediction_meta.py +306 -0
  334. endoreg_db/models/product/__init__.py +14 -0
  335. endoreg_db/models/product/product.py +110 -0
  336. endoreg_db/models/product/product_group.py +27 -0
  337. endoreg_db/models/product/product_material.py +28 -0
  338. endoreg_db/models/product/product_weight.py +38 -0
  339. endoreg_db/models/product/reference_product.py +115 -0
  340. endoreg_db/models/questionnaires/__init__.py +114 -0
  341. endoreg_db/models/quiz/__init__.py +9 -0
  342. endoreg_db/models/quiz/quiz_answer.py +41 -0
  343. endoreg_db/models/quiz/quiz_question.py +54 -0
  344. endoreg_db/models/report_reader/__init__.py +7 -0
  345. endoreg_db/models/report_reader/report_reader_config.py +53 -0
  346. endoreg_db/models/report_reader/report_reader_flag.py +20 -0
  347. endoreg_db/models/rules/__init__.py +5 -0
  348. endoreg_db/models/rules/rule.py +24 -0
  349. endoreg_db/models/rules/rule_applicator.py +224 -0
  350. endoreg_db/models/rules/rule_attribute_dtype.py +19 -0
  351. endoreg_db/models/rules/rule_type.py +22 -0
  352. endoreg_db/models/rules/ruleset.py +19 -0
  353. endoreg_db/models/unit.py +22 -0
  354. endoreg_db/queries/__init__.py +5 -0
  355. endoreg_db/queries/annotations/__init__.py +3 -0
  356. endoreg_db/queries/annotations/legacy.py +158 -0
  357. endoreg_db/queries/get/__init__.py +6 -0
  358. endoreg_db/queries/get/annotation.py +0 -0
  359. endoreg_db/queries/get/center.py +42 -0
  360. endoreg_db/queries/get/model.py +13 -0
  361. endoreg_db/queries/get/patient.py +14 -0
  362. endoreg_db/queries/get/patient_examination.py +20 -0
  363. endoreg_db/queries/get/prediction.py +0 -0
  364. endoreg_db/queries/get/report_file.py +33 -0
  365. endoreg_db/queries/get/video.py +31 -0
  366. endoreg_db/queries/get/video_import_meta.py +0 -0
  367. endoreg_db/queries/get/video_prediction_meta.py +0 -0
  368. endoreg_db/queries/sanity/__init_.py +0 -0
  369. endoreg_db/serializers/__init__.py +10 -0
  370. endoreg_db/serializers/ai_model.py +19 -0
  371. endoreg_db/serializers/annotation.py +14 -0
  372. endoreg_db/serializers/center.py +11 -0
  373. endoreg_db/serializers/examination.py +33 -0
  374. endoreg_db/serializers/frame.py +9 -0
  375. endoreg_db/serializers/hardware.py +21 -0
  376. endoreg_db/serializers/label.py +22 -0
  377. endoreg_db/serializers/patient.py +33 -0
  378. endoreg_db/serializers/prediction.py +10 -0
  379. endoreg_db/serializers/raw_video_meta_validation.py +13 -0
  380. endoreg_db/serializers/report_file.py +7 -0
  381. endoreg_db/serializers/video.py +20 -0
  382. endoreg_db/serializers/video_segmentation.py +492 -0
  383. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  384. endoreg_db/templates/admin/start_examination.html +12 -0
  385. endoreg_db/templates/timeline.html +176 -0
  386. endoreg_db/utils/__init__.py +36 -0
  387. endoreg_db/utils/cropping.py +29 -0
  388. endoreg_db/utils/dataloader.py +118 -0
  389. endoreg_db/utils/dates.py +39 -0
  390. endoreg_db/utils/file_operations.py +30 -0
  391. endoreg_db/utils/hashs.py +152 -0
  392. endoreg_db/utils/legacy_ocr.py +201 -0
  393. endoreg_db/utils/names.py +74 -0
  394. endoreg_db/utils/ocr.py +190 -0
  395. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  396. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  397. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  398. endoreg_db/utils/uuid.py +4 -0
  399. endoreg_db/utils/validate_endo_roi.py +19 -0
  400. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  401. endoreg_db/utils/video/__init__.py +13 -0
  402. endoreg_db/utils/video/extract_frames.py +121 -0
  403. endoreg_db/utils/video/transcode_videofile.py +111 -0
  404. endoreg_db/views/__init__.py +2 -0
  405. endoreg_db/views/csrf.py +7 -0
  406. endoreg_db/views/patient_views.py +90 -0
  407. endoreg_db/views/raw_video_meta_validation_views.py +38 -0
  408. endoreg_db/views/report_views.py +96 -0
  409. endoreg_db/views/video_segmentation_views.py +149 -0
  410. endoreg_db/views/views_for_timeline.py +46 -0
  411. {endoreg_db-0.6.0.dist-info → endoreg_db-0.6.2.dist-info}/METADATA +14 -4
  412. endoreg_db-0.6.2.dist-info/RECORD +420 -0
  413. {endoreg_db-0.6.0.dist-info → endoreg_db-0.6.2.dist-info}/WHEEL +1 -2
  414. endoreg_db-0.6.0.dist-info/RECORD +0 -11
  415. endoreg_db-0.6.0.dist-info/top_level.txt +0 -1
  416. {endoreg_db-0.6.0.dist-info → endoreg_db-0.6.2.dist-info/licenses}/LICENSE +0 -0
@@ -0,0 +1,59 @@
1
+ from django.conf import settings
2
+ from django.core.management.base import BaseCommand
3
+ from ...models import Label, LabelType, LabelSet
4
+ import os
5
+ from ...utils import load_model_data_from_yaml
6
+ from ...data import LABEL_DATA_DIR
7
+
8
+ SOURCE_DIR = LABEL_DATA_DIR
9
+
10
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
11
+ "LabelType",
12
+ "Label",
13
+ "LabelSet",
14
+ ]
15
+
16
+ IMPORT_METADATA = {
17
+ # "": { # same as model name in "import models", e.g. "Intervention"
18
+ # "subdir": os.path.join(SOURCE_DIR,""), # e.g. "interventions"
19
+ # "model": None, # e.g. Intervention
20
+ # "foreign_keys": [], # e.g. ["intervention_types"]
21
+ # "foreign_key_models": [] # e.g. [InterventionType]
22
+ # },
23
+ "LabelType": {
24
+ "dir": os.path.join(SOURCE_DIR, "label-type"), # e.g. "interventions"
25
+ "model": LabelType, # e.g. Intervention
26
+ "foreign_keys": [], # e.g. ["intervention_types"]
27
+ "foreign_key_models": [], # e.g. [InterventionType]
28
+ },
29
+ "Label": {
30
+ "dir": os.path.join(SOURCE_DIR, "label"), # e.g. "interventions"
31
+ "model": Label, # e.g. Intervention
32
+ "foreign_keys": ["label_type"], # e.g. ["intervention_types"]
33
+ "foreign_key_models": [LabelType], # e.g. [InterventionType]
34
+ },
35
+ "LabelSet": {
36
+ "dir": os.path.join(SOURCE_DIR, "label-set"), # e.g. "interventions"
37
+ "model": LabelSet, # e.g. Intervention
38
+ "foreign_keys": ["labels"], # e.g. ["intervention_types"]
39
+ "foreign_key_models": [Label], # e.g. [InterventionType]
40
+ },
41
+ }
42
+
43
+
44
+ class Command(BaseCommand):
45
+ help = """Load all .yaml files in the data/intervention directory
46
+ into the Intervention and InterventionType model"""
47
+
48
+ def add_arguments(self, parser):
49
+ parser.add_argument(
50
+ "--verbose",
51
+ action="store_true",
52
+ help="Display verbose output",
53
+ )
54
+
55
+ def handle(self, *args, **options):
56
+ verbose = options["verbose"]
57
+ for model_name in IMPORT_MODELS:
58
+ _metadata = IMPORT_METADATA[model_name]
59
+ load_model_data_from_yaml(self, model_name, _metadata, verbose)
@@ -0,0 +1,178 @@
1
+ from django.core.management import BaseCommand, call_command
2
+ from io import StringIO
3
+
4
+
5
+ class Command(BaseCommand):
6
+ help = "Run all data loading commands in the correct order"
7
+
8
+ def add_arguments(self, parser):
9
+ parser.add_argument(
10
+ "--verbose",
11
+ action="store_true",
12
+ help="Display verbose output for all commands",
13
+ )
14
+
15
+ def handle(self, *args, **options):
16
+ # verbose = options['verbose']
17
+ verbose = True
18
+
19
+ self.stdout.write(self.style.SUCCESS("Populating base db models with data..."))
20
+
21
+ out = self.stdout
22
+
23
+ # Load Center Data
24
+ call_command("load_center_data", stdout=out, verbose=verbose)
25
+ call_command("load_endoscope_data", stdout=out, verbose=verbose)
26
+ call_command("load_distribution_data", stdout=out, verbose=verbose)
27
+
28
+ call_command("load_gender_data", stdout=out, verbose=verbose)
29
+ call_command("load_report_reader_flag_data", stdout=out, verbose=verbose)
30
+ call_command("load_pdf_type_data", stdout=out, verbose=verbose)
31
+ call_command("load_unit_data", stdout=out, verbose=verbose)
32
+ call_command("load_disease_data", stdout=out, verbose=verbose)
33
+ call_command("load_event_data", stdout=out, verbose=verbose)
34
+ call_command("load_organ_data", stdout=out, verbose=verbose)
35
+ call_command("load_contraindication_data", stdout=out, verbose=verbose)
36
+ call_command("load_examination_data", stdout=out, verbose=verbose)
37
+ call_command("load_examination_indication_data", stdout=out, verbose=verbose)
38
+ call_command("load_lab_value_data", stdout=out, verbose=verbose)
39
+ call_command("load_finding_data", stdout=out, verbose=verbose)
40
+ call_command("load_medication_data", stdout=out, verbose=verbose)
41
+
42
+ # Load AI Model Data
43
+ call_command("load_ai_model_label_data", stdout=out, verbose=verbose)
44
+ call_command("load_ai_model_data", stdout=out, verbose=verbose)
45
+
46
+ self.stdout.write(
47
+ self.style.SUCCESS( # pylint: disable=no-member
48
+ "All data loading commands executed successfully."
49
+ )
50
+ )
51
+
52
+ # # Run the load_network_data command
53
+ # self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
54
+ # call_command('load_network_data', verbose=verbose)
55
+ # Run the load_network_data command
56
+ # self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
57
+ # call_command("load_network_data", verbose=verbose)
58
+
59
+ # # Run the load_logging_data command
60
+ # self.stdout.write(self.style.SUCCESS("Running load_logging_data..."))
61
+ # call_command("load_logging_data", verbose=verbose)
62
+
63
+ # # Run the load_profession_data command
64
+ # self.stdout.write(self.style.SUCCESS("Running load_profession_data..."))
65
+ # call_command("load_profession_data", verbose=verbose)
66
+
67
+ # # run the load_gender_data command
68
+ # self.stdout.write(self.style.SUCCESS("Running load_gender_data..."))
69
+ # call_command("load_gender_data", verbose=verbose)
70
+
71
+ # # Run the load_examination_data command
72
+ # self.stdout.write(self.style.SUCCESS("Running load_examination_data..."))
73
+ # call_command("load_examination_data", verbose=verbose)
74
+
75
+ # # run the load_finding_data command
76
+ # self.stdout.write(self.style.SUCCESS("Running load_finding_data..."))
77
+ # call_command("load_finding_data", verbose=verbose)
78
+
79
+ # # Run the load_disease data command
80
+ # self.stdout.write(self.style.SUCCESS("Running load_disease_data..."))
81
+ # call_command("load_disease_data", verbose=verbose)
82
+
83
+ # # # Run the load_disease_classification data command
84
+ # # self.stdout.write(self.style.SUCCESS("Running load_disease_classification_data..."))
85
+ # # call_command('load_disease_classification_data', verbose=verbose)
86
+
87
+ # # # Run the load_disease_classification_choices data command
88
+ # # self.stdout.write(self.style.SUCCESS("Running load_disease_classification_choices_data..."))
89
+ # # call_command('load_disease_classification_choices_data', verbose=verbose)
90
+
91
+ # # rund the load_user_groups command
92
+ # self.stdout.write(self.style.SUCCESS("Running load_user_groups..."))
93
+ # call_command("load_user_groups", verbose=verbose)
94
+
95
+ # # run the load_report_reader_flag command
96
+ # self.stdout.write(self.style.SUCCESS("Running load_report_reader_flag..."))
97
+ # call_command("load_report_reader_flag", verbose=verbose)
98
+
99
+ # # Run the load_pdf_type_data command
100
+ # self.stdout.write(self.style.SUCCESS("Running load_pdf_type_data..."))
101
+ # call_command("load_pdf_type_data", verbose=verbose)
102
+
103
+ # # Run the load_endoscopy_processor_data command
104
+ # self.stdout.write(
105
+ # self.style.SUCCESS("Running load_endoscopy_processor_data...")
106
+ # )
107
+ # call_command("load_endoscopy_processor_data", verbose=verbose)
108
+
109
+ # # Run the load_endoscope_type_data command
110
+ # self.stdout.write(self.style.SUCCESS("Running load_endoscope_type_data..."))
111
+ # call_command("load_endoscope_type_data", verbose=verbose)
112
+
113
+ # # Run the load_unit_data command
114
+ # self.stdout.write(self.style.SUCCESS("Running load_unit_data..."))
115
+ # call_command("load_unit_data", verbose=verbose)
116
+
117
+ # # Run the load_lab_value_data command
118
+ # self.stdout.write(self.style.SUCCESS("Running load_lab_value_data..."))
119
+ # call_command("load_lab_value_data", verbose=verbose)
120
+
121
+ # # Run the load_information_source command
122
+ # self.stdout.write(self.style.SUCCESS("Running load_information_source..."))
123
+ # call_command("load_information_source", verbose=verbose)
124
+
125
+ # # Run the load_center_data command
126
+ # self.stdout.write(self.style.SUCCESS("Running load_center_data..."))
127
+ # call_command("load_center_data", verbose=verbose)
128
+
129
+ # # Run the load_label_data command
130
+ # self.stdout.write(self.style.SUCCESS("Running load_label_data..."))
131
+ # call_command("load_label_data", verbose=verbose)
132
+
133
+ # # Run the load_ai_model_data command
134
+ # self.stdout.write(self.style.SUCCESS("Running load_ai_model_data..."))
135
+ # call_command("load_ai_model_data", verbose=verbose)
136
+
137
+ # # Run the load_event_data command
138
+ # self.stdout.write(self.style.SUCCESS("Running load_event_data..."))
139
+ # call_command("load_event_data", verbose=verbose)
140
+
141
+ # # run the load_medication_data command
142
+ # self.stdout.write(self.style.SUCCESS("Running load_medication_data..."))
143
+ # call_command("load_medication_data", verbose=verbose)
144
+
145
+ # # # Run the load_medication_indication_type_data command
146
+ # # self.stdout.write(self.style.SUCCESS("Running load_medication_indication_type_data..."))
147
+ # # call_command('load_medication_indication_type_data', verbose=verbose)
148
+
149
+ # # # Run the load_medication_intake_time_data command
150
+ # # self.stdout.write(self.style.SUCCESS("Running load_medication_intake_time_data..."))
151
+ # # call_command('load_medication_intake_time_data', verbose=verbose)
152
+
153
+ # # # Run the load_medication_schedule_data command
154
+ # # self.stdout.write(self.style.SUCCESS("Running load_medication_schedule_data..."))
155
+ # # call_command('load_medication_schedule_data', verbose=verbose)
156
+
157
+ # # # Run the load_medication_indication_data command
158
+ # # self.stdout.write(self.style.SUCCESS("Running load_medication_indication_data..."))
159
+ # # call_command('load_medication_indication_data', verbose=verbose)
160
+
161
+ # # Run the load_green_endoscopy_wuerzburg_data command
162
+ # self.stdout.write(
163
+ # self.style.SUCCESS("Running load_green_endoscopy_wuerzburg_data...")
164
+ # )
165
+ # call_command("load_green_endoscopy_wuerzburg_data", verbose=verbose)
166
+
167
+ # # Load G-Play Data
168
+ # # run the load_distribution_data command
169
+ # self.stdout.write(self.style.SUCCESS("Running load_distribution_data..."))
170
+ # call_command("load_distribution_data", verbose=verbose)
171
+ # # Run the load_g_play_data command
172
+ # self.stdout.write(self.style.SUCCESS("Running load_g_play_data..."))
173
+ # call_command("load_g_play_data", verbose=verbose)
174
+
175
+ # # Necessary? Migrate? FIXME
176
+ # # # Run the load_active_model_data command
177
+ # # self.stdout.write(self.style.SUCCESS("Running load_active_model_data..."))
178
+ # # call_command('load_active_model_data', verbose=verbose)
@@ -0,0 +1,43 @@
1
+ from django.core.management.base import BaseCommand
2
+ from ...utils import load_model_data_from_yaml
3
+ from ...models import Center, FirstName, LastName
4
+ from ...data import CENTER_DATA_DIR
5
+
6
+ SOURCE_DIR = CENTER_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
7
+
8
+ MODEL_0 = Center
9
+
10
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
11
+ MODEL_0.__name__,
12
+ ]
13
+
14
+ IMPORT_METADATA = {
15
+ MODEL_0.__name__: {
16
+ "dir": SOURCE_DIR, # e.g. "interventions"
17
+ "model": MODEL_0, # e.g. Intervention
18
+ "foreign_keys": ["first_names", "last_names"], # e.g. ["intervention_types"]
19
+ "foreign_key_models": [FirstName, LastName] # e.g. [InterventionType]
20
+ }
21
+ }
22
+
23
+ class Command(BaseCommand):
24
+ help = """Load all .yaml files in the data/intervention directory
25
+ into the Intervention and InterventionType model"""
26
+
27
+ def add_arguments(self, parser):
28
+ parser.add_argument(
29
+ '--verbose',
30
+ action='store_true',
31
+ help='Display verbose output',
32
+ )
33
+
34
+ def handle(self, *args, **options):
35
+ verbose = options['verbose']
36
+ for model_name in IMPORT_MODELS:
37
+ _metadata = IMPORT_METADATA[model_name]
38
+ load_model_data_from_yaml(
39
+ self,
40
+ model_name,
41
+ _metadata,
42
+ verbose
43
+ )
@@ -0,0 +1,41 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import Contraindication
3
+ from ...utils import load_model_data_from_yaml
4
+ from ...data import CONTRAINDICATION_DATA_DIR as SOURCE_DIR
5
+
6
+ MODEL_0 = Contraindication
7
+
8
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
9
+ MODEL_0.__name__,
10
+ ]
11
+
12
+ IMPORT_METADATA = {
13
+ MODEL_0.__name__: {
14
+ "dir": SOURCE_DIR, # e.g. "interventions"
15
+ "model": MODEL_0, # e.g. Intervention
16
+ "foreign_keys": [], # e.g. ["intervention_types"]
17
+ "foreign_key_models": [] # e.g. [InterventionType]
18
+ }
19
+ }
20
+
21
+ class Command(BaseCommand):
22
+ help = """Load all .yaml files in the data/intervention directory
23
+ into the Intervention and InterventionType model"""
24
+
25
+ def add_arguments(self, parser):
26
+ parser.add_argument(
27
+ '--verbose',
28
+ action='store_true',
29
+ help='Display verbose output',
30
+ )
31
+
32
+ def handle(self, *args, **options):
33
+ verbose = options['verbose']
34
+ for model_name in IMPORT_MODELS:
35
+ _metadata = IMPORT_METADATA[model_name]
36
+ load_model_data_from_yaml(
37
+ self,
38
+ model_name,
39
+ _metadata,
40
+ verbose
41
+ )
@@ -0,0 +1,41 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import DiseaseClassificationChoice as MODEL_0
3
+ from ...utils import load_model_data_from_yaml
4
+ from ...data import DISEASE_CLASSIFICATION_CHOICE_DATA_DIR as SOURCE_DIR
5
+
6
+ from endoreg_db.models import DiseaseClassification
7
+
8
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
9
+ MODEL_0.__name__,
10
+ ]
11
+
12
+ IMPORT_METADATA = {
13
+ MODEL_0.__name__: {
14
+ "dir": SOURCE_DIR, # e.g. "interventions"
15
+ "model": MODEL_0, # e.g. Intervention
16
+ "foreign_keys": ["disease_classification"], # e.g. ["intervention_types"]
17
+ "foreign_key_models": [DiseaseClassification] # e.g. [InterventionType]
18
+ }
19
+ }
20
+
21
+ class Command(BaseCommand):
22
+ help = """Load all .yaml files in the data/intervention directory
23
+ into the Intervention and InterventionType model"""
24
+
25
+ def add_arguments(self, parser):
26
+ parser.add_argument(
27
+ '--verbose',
28
+ action='store_true',
29
+ help='Display verbose output',
30
+ )
31
+
32
+ def handle(self, *args, **options):
33
+ verbose = options['verbose']
34
+ for model_name in IMPORT_MODELS:
35
+ _metadata = IMPORT_METADATA[model_name]
36
+ load_model_data_from_yaml(
37
+ self,
38
+ model_name,
39
+ _metadata,
40
+ verbose
41
+ )
@@ -0,0 +1,41 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import DiseaseClassification as MODEL_0
3
+ from ...utils import load_model_data_from_yaml
4
+ from ...data import DISEASE_CLASSIFICATION_DATA_DIR as SOURCE_DIR
5
+
6
+ from endoreg_db.models import Disease
7
+
8
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
9
+ MODEL_0.__name__,
10
+ ]
11
+
12
+ IMPORT_METADATA = {
13
+ MODEL_0.__name__: {
14
+ "dir": SOURCE_DIR, # e.g. "interventions"
15
+ "model": MODEL_0, # e.g. Intervention
16
+ "foreign_keys": ["disease"], # e.g. ["intervention_types"]
17
+ "foreign_key_models": [Disease] # e.g. [InterventionType]
18
+ }
19
+ }
20
+
21
+ class Command(BaseCommand):
22
+ help = """Load all .yaml files in the data/intervention directory
23
+ into the Intervention and InterventionType model"""
24
+
25
+ def add_arguments(self, parser):
26
+ parser.add_argument(
27
+ '--verbose',
28
+ action='store_true',
29
+ help='Display verbose output',
30
+ )
31
+
32
+ def handle(self, *args, **options):
33
+ verbose = options['verbose']
34
+ for model_name in IMPORT_MODELS:
35
+ _metadata = IMPORT_METADATA[model_name]
36
+ load_model_data_from_yaml(
37
+ self,
38
+ model_name,
39
+ _metadata,
40
+ verbose
41
+ )
@@ -0,0 +1,62 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import (
3
+ Disease,
4
+ DiseaseClassification,
5
+ DiseaseClassificationChoice,
6
+ )
7
+ from ...utils import load_model_data_from_yaml
8
+ from ...data import (
9
+ DISEASE_DATA_DIR,
10
+ DISEASE_CLASSIFICATION_DATA_DIR,
11
+ DISEASE_CLASSIFICATION_CHOICE_DATA_DIR,
12
+ )
13
+
14
+
15
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
16
+ Disease.__name__,
17
+ DiseaseClassification.__name__,
18
+ DiseaseClassificationChoice.__name__,
19
+ ]
20
+
21
+ IMPORT_METADATA = {
22
+ Disease.__name__: {
23
+ "dir": DISEASE_DATA_DIR, # e.g. "interventions"
24
+ "model": Disease, # e.g. Intervention
25
+ "foreign_keys": [], # e.g. ["intervention_types"]
26
+ "foreign_key_models": [] # e.g. [InterventionType]
27
+ },
28
+ DiseaseClassification.__name__: {
29
+ "dir": DISEASE_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
30
+ "model": DiseaseClassification, # e.g. Intervention
31
+ "foreign_keys": ["disease"], # e.g. ["intervention_types"]
32
+ "foreign_key_models": [Disease] # e.g. [InterventionType]
33
+ },
34
+ DiseaseClassificationChoice.__name__: {
35
+ "dir": DISEASE_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
36
+ "model": DiseaseClassificationChoice, # e.g. Intervention
37
+ "foreign_keys": ["disease_classification"], # e.g. ["intervention_types"]
38
+ "foreign_key_models": [DiseaseClassification] # e.g. [InterventionType]
39
+ },
40
+ }
41
+
42
+ class Command(BaseCommand):
43
+ help = """Load all .yaml files in the data/intervention directory
44
+ into the Intervention and InterventionType model"""
45
+
46
+ def add_arguments(self, parser):
47
+ parser.add_argument(
48
+ '--verbose',
49
+ action='store_true',
50
+ help='Display verbose output',
51
+ )
52
+
53
+ def handle(self, *args, **options):
54
+ verbose = options['verbose']
55
+ for model_name in IMPORT_MODELS:
56
+ _metadata = IMPORT_METADATA[model_name]
57
+ load_model_data_from_yaml(
58
+ self,
59
+ model_name,
60
+ _metadata,
61
+ verbose
62
+ )
@@ -0,0 +1,66 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import (
3
+ NumericValueDistribution,
4
+ SingleCategoricalValueDistribution,
5
+ MultipleCategoricalValueDistribution,
6
+ DateValueDistribution
7
+
8
+ )
9
+ from collections import OrderedDict
10
+
11
+ from ...utils import load_model_data_from_yaml
12
+ from ...data import (
13
+ DISTRIBUTION_NUMERIC_DATA_DIR,
14
+ DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR,
15
+ DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR,
16
+ DISTRIBUTION_DATE_DATA_DIR,
17
+ )
18
+
19
+ IMPORT_METADATA = OrderedDict({
20
+ NumericValueDistribution.__name__: {
21
+ "dir": DISTRIBUTION_NUMERIC_DATA_DIR,
22
+ "model": NumericValueDistribution,
23
+ "foreign_keys": [],
24
+ "foreign_key_models": []
25
+ },
26
+ SingleCategoricalValueDistribution.__name__: {
27
+ "dir": DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR,
28
+ "model": SingleCategoricalValueDistribution,
29
+ "foreign_keys": [],
30
+ "foreign_key_models": []
31
+ },
32
+ MultipleCategoricalValueDistribution.__name__: {
33
+ "dir": DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR,
34
+ "model": MultipleCategoricalValueDistribution,
35
+ "foreign_keys": [],
36
+ "foreign_key_models": []
37
+ },
38
+ DateValueDistribution.__name__: {
39
+ "dir": DISTRIBUTION_DATE_DATA_DIR,
40
+ "model": DateValueDistribution,
41
+ "foreign_keys": [],
42
+ "foreign_key_models": []
43
+ },
44
+ })
45
+
46
+ class Command(BaseCommand):
47
+ help = """Load all .yaml files in the data/intervention directory
48
+ into the Intervention and InterventionType model"""
49
+
50
+ def add_arguments(self, parser):
51
+ parser.add_argument(
52
+ '--verbose',
53
+ action='store_true',
54
+ help='Display verbose output',
55
+ )
56
+
57
+ def handle(self, *args, **options):
58
+ verbose = options['verbose']
59
+ for model_name in IMPORT_METADATA.keys():
60
+ _metadata = IMPORT_METADATA[model_name]
61
+ load_model_data_from_yaml(
62
+ self,
63
+ model_name,
64
+ _metadata,
65
+ verbose
66
+ )
@@ -0,0 +1,68 @@
1
+ from django.conf import settings
2
+ import os
3
+ from django.core.management.base import BaseCommand
4
+ from ...models import (
5
+ EndoscopeType,
6
+ Endoscope,
7
+ EndoscopyProcessor,
8
+ Center
9
+ )
10
+ from ...utils import load_model_data_from_yaml
11
+ from ...data import (
12
+ ENDOSCOPE_TYPE_DATA_DIR,
13
+ ENDOSCOPY_PROCESSOR_DATA_DIR,
14
+ ENDOSCOPE_DATA_DIR,
15
+ )
16
+
17
+ SOURCE_DIR = ENDOSCOPE_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
18
+
19
+ MODEL_0 = EndoscopeType
20
+
21
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
22
+ EndoscopeType.__name__,
23
+ EndoscopyProcessor.__name__,
24
+ Endoscope.__name__,
25
+ ]
26
+
27
+ IMPORT_METADATA = {
28
+ EndoscopeType.__name__: {
29
+ "dir": ENDOSCOPE_TYPE_DATA_DIR, # e.g. "interventions"
30
+ "model": EndoscopeType, # e.g. Intervention
31
+ "foreign_keys": [], # e.g. ["intervention_types"]
32
+ "foreign_key_models": [] # e.g. [InterventionType]
33
+ },
34
+ EndoscopyProcessor.__name__: {
35
+ "dir": ENDOSCOPY_PROCESSOR_DATA_DIR,
36
+ "model": EndoscopyProcessor,
37
+ "foreign_keys": [],
38
+ "foreign_key_models": []
39
+ },
40
+ Endoscope.__name__: {
41
+ "dir": ENDOSCOPE_DATA_DIR,
42
+ "model": Endoscope,
43
+ "foreign_keys": ["center", "endoscope_type"],
44
+ "foreign_key_models": [Center, EndoscopeType]
45
+ },
46
+ }
47
+
48
+ class Command(BaseCommand):
49
+ help = """Load all .yaml files in the data/intervention directory
50
+ into the Intervention and InterventionType model"""
51
+
52
+ def add_arguments(self, parser):
53
+ parser.add_argument(
54
+ '--verbose',
55
+ action='store_true',
56
+ help='Display verbose output',
57
+ )
58
+
59
+ def handle(self, *args, **options):
60
+ verbose = options['verbose']
61
+ for model_name in IMPORT_MODELS:
62
+ _metadata = IMPORT_METADATA[model_name]
63
+ load_model_data_from_yaml(
64
+ self,
65
+ model_name,
66
+ _metadata,
67
+ verbose
68
+ )
@@ -0,0 +1,41 @@
1
+ from django.core.management.base import BaseCommand
2
+ from endoreg_db.models import Event
3
+ from ...utils import load_model_data_from_yaml
4
+ from ...data import EVENT_DATA_DIR as SOURCE_DIR
5
+
6
+ MODEL_0 = Event
7
+
8
+ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
9
+ MODEL_0.__name__,
10
+ ]
11
+
12
+ IMPORT_METADATA = {
13
+ MODEL_0.__name__: {
14
+ "dir": SOURCE_DIR, # e.g. "interventions"
15
+ "model": MODEL_0, # e.g. Intervention
16
+ "foreign_keys": [], # e.g. ["intervention_types"]
17
+ "foreign_key_models": [] # e.g. [InterventionType]
18
+ }
19
+ }
20
+
21
+ class Command(BaseCommand):
22
+ help = """Load all .yaml files in the data/intervention directory
23
+ into the Intervention and InterventionType model"""
24
+
25
+ def add_arguments(self, parser):
26
+ parser.add_argument(
27
+ '--verbose',
28
+ action='store_true',
29
+ help='Display verbose output',
30
+ )
31
+
32
+ def handle(self, *args, **options):
33
+ verbose = options['verbose']
34
+ for model_name in IMPORT_MODELS:
35
+ _metadata = IMPORT_METADATA[model_name]
36
+ load_model_data_from_yaml(
37
+ self,
38
+ model_name,
39
+ _metadata,
40
+ verbose
41
+ )