endoreg-db 0.8.5.1__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/admin.py +92 -0
  3. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  4. endoreg_db/api/views/finding_descriptions.py +0 -0
  5. endoreg_db/api_urls.py +4 -0
  6. endoreg_db/apps.py +18 -0
  7. endoreg_db/assets/dummy_model.ckpt +1 -0
  8. endoreg_db/codemods/readme.md +88 -0
  9. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  10. endoreg_db/config/__init__.py +0 -0
  11. endoreg_db/config/env.py +101 -0
  12. endoreg_db/data/__init__.py +144 -0
  13. endoreg_db/data/ai_model/data.yaml +7 -0
  14. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  15. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  16. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  17. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  18. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  19. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  20. endoreg_db/data/ai_model_type/data.yaml +7 -0
  21. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  22. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  23. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  24. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  25. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  26. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  27. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  28. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  29. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  30. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  31. endoreg_db/data/case_template/rule_value/.init +0 -0
  32. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  33. endoreg_db/data/case_template/template/base.yaml +8 -0
  34. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  35. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  36. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  37. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  38. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  39. endoreg_db/data/center/data.yaml +91 -0
  40. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  41. endoreg_db/data/center_shift/ukw.yaml +9 -0
  42. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  43. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  44. endoreg_db/data/db_summary.csv +58 -0
  45. endoreg_db/data/db_summary.xlsx +0 -0
  46. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  47. endoreg_db/data/disease/hepatology.yaml +5 -0
  48. endoreg_db/data/disease/misc.yaml +5 -0
  49. endoreg_db/data/disease/renal.yaml +5 -0
  50. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  51. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  52. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  53. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  54. endoreg_db/data/distribution/date/patient.yaml +7 -0
  55. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  56. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  57. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  58. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  59. endoreg_db/data/endoscope/data.yaml +93 -0
  60. endoreg_db/data/endoscope_type/data.yaml +11 -0
  61. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  62. endoreg_db/data/event/cardiology.yaml +15 -0
  63. endoreg_db/data/event/neurology.yaml +14 -0
  64. endoreg_db/data/event/surgery.yaml +13 -0
  65. endoreg_db/data/event/thrombembolism.yaml +20 -0
  66. endoreg_db/data/examination/examinations/data.yaml +72 -0
  67. endoreg_db/data/examination/time/data.yaml +48 -0
  68. endoreg_db/data/examination/time-type/data.yaml +8 -0
  69. endoreg_db/data/examination/type/data.yaml +17 -0
  70. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  71. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  72. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  73. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  74. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  75. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  76. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  77. endoreg_db/data/finding/complication.yaml +16 -0
  78. endoreg_db/data/finding/data.yaml +105 -0
  79. endoreg_db/data/finding/examination_setting.yaml +16 -0
  80. endoreg_db/data/finding/medication_related.yaml +18 -0
  81. endoreg_db/data/finding/outcome.yaml +12 -0
  82. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  83. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  84. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  85. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  87. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  88. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  89. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  90. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  91. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  92. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  93. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  94. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  95. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  96. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  97. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  98. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  99. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  100. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  101. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  105. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  106. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  107. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  108. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  109. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  110. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  111. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  112. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  114. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  115. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  116. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  117. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  118. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  119. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  120. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  121. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  122. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  123. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  124. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  125. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  126. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  127. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  128. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  129. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  130. endoreg_db/data/finding_type/data.yaml +43 -0
  131. endoreg_db/data/gender/data.yaml +42 -0
  132. endoreg_db/data/information_source/annotation.yaml +6 -0
  133. endoreg_db/data/information_source/data.yaml +30 -0
  134. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  135. endoreg_db/data/information_source/medication.yaml +6 -0
  136. endoreg_db/data/information_source/prediction.yaml +7 -0
  137. endoreg_db/data/information_source_type/data.yaml +8 -0
  138. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  139. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  140. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  141. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  142. endoreg_db/data/lab_value/hematology.yaml +184 -0
  143. endoreg_db/data/lab_value/hormones.yaml +59 -0
  144. endoreg_db/data/lab_value/lipids.yaml +53 -0
  145. endoreg_db/data/lab_value/misc.yaml +76 -0
  146. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  147. endoreg_db/data/log_type/data.yaml +57 -0
  148. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  149. endoreg_db/data/lx_client_type/base.yaml +30 -0
  150. endoreg_db/data/lx_permission/base.yaml +24 -0
  151. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  152. endoreg_db/data/material/material.yaml +91 -0
  153. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  154. endoreg_db/data/medication/tah.yaml +70 -0
  155. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  156. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  157. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  158. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  159. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  160. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  161. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  162. endoreg_db/data/names_first/first_names.yaml +54 -0
  163. endoreg_db/data/names_last/last_names.yaml +51 -0
  164. endoreg_db/data/network_device/data.yaml +59 -0
  165. endoreg_db/data/network_device_type/data.yaml +12 -0
  166. endoreg_db/data/organ/data.yaml +29 -0
  167. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  168. endoreg_db/data/pdf_type/data.yaml +46 -0
  169. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  170. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  171. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  172. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  173. endoreg_db/data/profession/data.yaml +70 -0
  174. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  175. endoreg_db/data/qualification/m2.yaml +39 -0
  176. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  177. endoreg_db/data/qualification/sonography.yaml +36 -0
  178. endoreg_db/data/qualification_type/base.yaml +29 -0
  179. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  180. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  181. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  182. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  183. endoreg_db/data/requirement/age.yaml +26 -0
  184. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  185. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  186. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  187. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  188. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  189. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  190. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  191. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  192. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  193. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  194. endoreg_db/data/requirement/gender.yaml +25 -0
  195. endoreg_db/data/requirement/lab_value.yaml +441 -0
  196. endoreg_db/data/requirement/medication.yaml +93 -0
  197. endoreg_db/data/requirement_operator/age.yaml +13 -0
  198. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  199. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  200. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  201. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  202. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  203. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  204. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  205. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  206. endoreg_db/data/risk/bleeding.yaml +26 -0
  207. endoreg_db/data/risk/thrombosis.yaml +37 -0
  208. endoreg_db/data/risk_type/data.yaml +27 -0
  209. endoreg_db/data/setup_config.yaml +38 -0
  210. endoreg_db/data/shift/endoscopy.yaml +21 -0
  211. endoreg_db/data/shift/m2.yaml +0 -0
  212. endoreg_db/data/shift_type/base.yaml +35 -0
  213. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  214. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  215. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  216. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  217. endoreg_db/data/unit/concentration.yaml +115 -0
  218. endoreg_db/data/unit/data.yaml +17 -0
  219. endoreg_db/data/unit/length.yaml +31 -0
  220. endoreg_db/data/unit/misc.yaml +20 -0
  221. endoreg_db/data/unit/rate.yaml +6 -0
  222. endoreg_db/data/unit/time.yaml +48 -0
  223. endoreg_db/data/unit/volume.yaml +35 -0
  224. endoreg_db/data/unit/weight.yaml +38 -0
  225. endoreg_db/data/waste/data.yaml +12 -0
  226. endoreg_db/exceptions.py +19 -0
  227. endoreg_db/factories/__init__.py +0 -0
  228. endoreg_db/forms/__init__.py +5 -0
  229. endoreg_db/forms/examination_form.py +11 -0
  230. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  231. endoreg_db/forms/patient_form.py +27 -0
  232. endoreg_db/forms/questionnaires/__init__.py +1 -0
  233. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  234. endoreg_db/forms/settings/__init__.py +8 -0
  235. endoreg_db/forms/unit.py +6 -0
  236. endoreg_db/helpers/__init__.py +0 -0
  237. endoreg_db/helpers/count_db.py +45 -0
  238. endoreg_db/helpers/data_loader.py +208 -0
  239. endoreg_db/helpers/default_objects.py +378 -0
  240. endoreg_db/helpers/download_segmentation_model.py +31 -0
  241. endoreg_db/helpers/interact.py +6 -0
  242. endoreg_db/helpers/test_video_helper.py +119 -0
  243. endoreg_db/logger_conf.py +140 -0
  244. endoreg_db/management/__init__.py +1 -0
  245. endoreg_db/management/commands/__init__.py +1 -0
  246. endoreg_db/management/commands/anonymize_video.py +0 -0
  247. endoreg_db/management/commands/check_auth.py +125 -0
  248. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  249. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  250. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  251. endoreg_db/management/commands/fix_video_paths.py +165 -0
  252. endoreg_db/management/commands/import_fallback_video.py +203 -0
  253. endoreg_db/management/commands/import_report.py +298 -0
  254. endoreg_db/management/commands/import_video.py +423 -0
  255. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  256. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  257. endoreg_db/management/commands/load_ai_model_data.py +77 -0
  258. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  259. endoreg_db/management/commands/load_base_db_data.py +192 -0
  260. endoreg_db/management/commands/load_center_data.py +68 -0
  261. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  262. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  263. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  264. endoreg_db/management/commands/load_disease_data.py +62 -0
  265. endoreg_db/management/commands/load_distribution_data.py +66 -0
  266. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  267. endoreg_db/management/commands/load_event_data.py +41 -0
  268. endoreg_db/management/commands/load_examination_data.py +75 -0
  269. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  270. endoreg_db/management/commands/load_finding_data.py +128 -0
  271. endoreg_db/management/commands/load_gender_data.py +44 -0
  272. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
  273. endoreg_db/management/commands/load_information_source.py +51 -0
  274. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  275. endoreg_db/management/commands/load_medication_data.py +103 -0
  276. endoreg_db/management/commands/load_name_data.py +37 -0
  277. endoreg_db/management/commands/load_organ_data.py +43 -0
  278. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  279. endoreg_db/management/commands/load_profession_data.py +44 -0
  280. endoreg_db/management/commands/load_qualification_data.py +59 -0
  281. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  282. endoreg_db/management/commands/load_requirement_data.py +180 -0
  283. endoreg_db/management/commands/load_risk_data.py +56 -0
  284. endoreg_db/management/commands/load_shift_data.py +60 -0
  285. endoreg_db/management/commands/load_tag_data.py +57 -0
  286. endoreg_db/management/commands/load_unit_data.py +46 -0
  287. endoreg_db/management/commands/load_user_groups.py +28 -0
  288. endoreg_db/management/commands/register_ai_model.py +64 -0
  289. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  290. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  291. endoreg_db/management/commands/start_filewatcher.py +106 -0
  292. endoreg_db/management/commands/storage_management.py +548 -0
  293. endoreg_db/management/commands/summarize_db_content.py +189 -0
  294. endoreg_db/management/commands/validate_video.py +204 -0
  295. endoreg_db/management/commands/validate_video_files.py +161 -0
  296. endoreg_db/management/commands/video_validation.py +22 -0
  297. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  298. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  299. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
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  607. endoreg_db/tasks/video_processing_tasks.py +327 -0
  608. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  609. endoreg_db/templates/admin/start_examination.html +12 -0
  610. endoreg_db/templates/timeline.html +176 -0
  611. endoreg_db/urls/__init__.py +70 -0
  612. endoreg_db/urls/anonymization.py +32 -0
  613. endoreg_db/urls/auth.py +16 -0
  614. endoreg_db/urls/classification.py +39 -0
  615. endoreg_db/urls/examination.py +54 -0
  616. endoreg_db/urls/files.py +6 -0
  617. endoreg_db/urls/label_video_segment_validate.py +33 -0
  618. endoreg_db/urls/label_video_segments.py +44 -0
  619. endoreg_db/urls/media.py +226 -0
  620. endoreg_db/urls/patient.py +19 -0
  621. endoreg_db/urls/report.py +48 -0
  622. endoreg_db/urls/requirements.py +13 -0
  623. endoreg_db/urls/sensitive_meta.py +0 -0
  624. endoreg_db/urls/stats.py +46 -0
  625. endoreg_db/urls/upload.py +20 -0
  626. endoreg_db/urls/video.py +61 -0
  627. endoreg_db/urls.py +9 -0
  628. endoreg_db/utils/__init__.py +88 -0
  629. endoreg_db/utils/ai/__init__.py +9 -0
  630. endoreg_db/utils/ai/get.py +5 -0
  631. endoreg_db/utils/ai/inference_dataset.py +52 -0
  632. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  633. endoreg_db/utils/ai/postprocess.py +63 -0
  634. endoreg_db/utils/ai/predict.py +291 -0
  635. endoreg_db/utils/ai/preprocess.py +68 -0
  636. endoreg_db/utils/calc_duration_seconds.py +24 -0
  637. endoreg_db/utils/case_generator/__init__.py +0 -0
  638. endoreg_db/utils/case_generator/case_generator.py +159 -0
  639. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  640. endoreg_db/utils/case_generator/utils.py +30 -0
  641. endoreg_db/utils/check_video_files.py +148 -0
  642. endoreg_db/utils/cropping.py +29 -0
  643. endoreg_db/utils/dataloader.py +175 -0
  644. endoreg_db/utils/dates.py +60 -0
  645. endoreg_db/utils/env.py +33 -0
  646. endoreg_db/utils/extract_specific_frames.py +72 -0
  647. endoreg_db/utils/file_operations.py +58 -0
  648. endoreg_db/utils/fix_video_path_direct.py +141 -0
  649. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  650. endoreg_db/utils/hashs.py +153 -0
  651. endoreg_db/utils/links/__init__.py +0 -0
  652. endoreg_db/utils/links/requirement_link.py +193 -0
  653. endoreg_db/utils/mime_types.py +0 -0
  654. endoreg_db/utils/names.py +76 -0
  655. endoreg_db/utils/ocr.py +190 -0
  656. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  657. endoreg_db/utils/paths.py +95 -0
  658. endoreg_db/utils/permissions.py +143 -0
  659. endoreg_db/utils/pipelines/Readme.md +235 -0
  660. endoreg_db/utils/pipelines/__init__.py +0 -0
  661. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  662. endoreg_db/utils/product/__init__.py +0 -0
  663. endoreg_db/utils/product/sum_emissions.py +20 -0
  664. endoreg_db/utils/product/sum_weights.py +18 -0
  665. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  666. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  667. endoreg_db/utils/requirement_helpers.py +0 -0
  668. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  669. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  670. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  671. endoreg_db/utils/setup_config.py +177 -0
  672. endoreg_db/utils/translation.py +27 -0
  673. endoreg_db/utils/uuid.py +4 -0
  674. endoreg_db/utils/validate_endo_roi.py +19 -0
  675. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  676. endoreg_db/utils/validate_video_detailed.py +357 -0
  677. endoreg_db/utils/video/__init__.py +26 -0
  678. endoreg_db/utils/video/extract_frames.py +88 -0
  679. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  680. endoreg_db/utils/video/names.py +42 -0
  681. endoreg_db/utils/video/streaming_processor.py +312 -0
  682. endoreg_db/utils/video/video_splitter.py +94 -0
  683. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  684. endoreg_db/views/__init__.py +272 -0
  685. endoreg_db/views/anonymization/__init__.py +27 -0
  686. endoreg_db/views/anonymization/media_management.py +454 -0
  687. endoreg_db/views/anonymization/overview.py +216 -0
  688. endoreg_db/views/anonymization/validate.py +107 -0
  689. endoreg_db/views/auth/__init__.py +13 -0
  690. endoreg_db/views/auth/keycloak.py +113 -0
  691. endoreg_db/views/examination/__init__.py +33 -0
  692. endoreg_db/views/examination/examination.py +37 -0
  693. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  694. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  695. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  696. endoreg_db/views/examination/get_findings.py +41 -0
  697. endoreg_db/views/examination/get_instruments.py +18 -0
  698. endoreg_db/views/examination/get_interventions.py +14 -0
  699. endoreg_db/views/finding/__init__.py +9 -0
  700. endoreg_db/views/finding/finding.py +112 -0
  701. endoreg_db/views/finding/get_classifications.py +14 -0
  702. endoreg_db/views/finding/get_interventions.py +17 -0
  703. endoreg_db/views/finding_classification/__init__.py +13 -0
  704. endoreg_db/views/finding_classification/base.py +0 -0
  705. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  706. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  707. endoreg_db/views/label/__init__.py +5 -0
  708. endoreg_db/views/label/label.py +15 -0
  709. endoreg_db/views/label_video_segment/__init__.py +16 -0
  710. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  711. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  712. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  713. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  715. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  716. endoreg_db/views/label_video_segment/validate.py +226 -0
  717. endoreg_db/views/media/__init__.py +45 -0
  718. endoreg_db/views/media/pdf_media.py +386 -0
  719. endoreg_db/views/media/segments.py +71 -0
  720. endoreg_db/views/media/sensitive_metadata.py +314 -0
  721. endoreg_db/views/media/video_media.py +272 -0
  722. endoreg_db/views/media/video_segments.py +524 -0
  723. endoreg_db/views/meta/__init__.py +15 -0
  724. endoreg_db/views/meta/available_files_list.py +146 -0
  725. endoreg_db/views/meta/report_meta.py +53 -0
  726. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  727. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  728. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  729. endoreg_db/views/misc/__init__.py +63 -0
  730. endoreg_db/views/misc/center.py +13 -0
  731. endoreg_db/views/misc/csrf.py +7 -0
  732. endoreg_db/views/misc/gender.py +14 -0
  733. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  734. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  735. endoreg_db/views/misc/secure_url_validate.py +79 -0
  736. endoreg_db/views/misc/stats.py +220 -0
  737. endoreg_db/views/misc/translation.py +182 -0
  738. endoreg_db/views/misc/upload_views.py +240 -0
  739. endoreg_db/views/patient/__init__.py +5 -0
  740. endoreg_db/views/patient/patient.py +210 -0
  741. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  742. endoreg_db/views/patient_examination/__init__.py +11 -0
  743. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  744. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  745. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  746. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  747. endoreg_db/views/patient_examination/video.py +194 -0
  748. endoreg_db/views/patient_finding/__init__.py +7 -0
  749. endoreg_db/views/patient_finding/base.py +0 -0
  750. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  751. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  752. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  753. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  754. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  755. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  756. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  758. endoreg_db/views/pdf/__init__.py +11 -0
  759. endoreg_db/views/pdf/pdf_media.py +239 -0
  760. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  761. endoreg_db/views/pdf/reimport.py +161 -0
  762. endoreg_db/views/report/__init__.py +9 -0
  763. endoreg_db/views/report/report_list.py +112 -0
  764. endoreg_db/views/report/report_with_secure_url.py +28 -0
  765. endoreg_db/views/report/start_examination.py +7 -0
  766. endoreg_db/views/requirement/__init__.py +10 -0
  767. endoreg_db/views/requirement/evaluate.py +279 -0
  768. endoreg_db/views/requirement/lookup.py +483 -0
  769. endoreg_db/views/requirement/lookup_store.py +252 -0
  770. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  771. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  772. endoreg_db/views/stats/__init__.py +13 -0
  773. endoreg_db/views/stats/stats_views.py +229 -0
  774. endoreg_db/views/video/__init__.py +61 -0
  775. endoreg_db/views/video/correction.py +530 -0
  776. endoreg_db/views/video/reimport.py +195 -0
  777. endoreg_db/views/video/segmentation.py +274 -0
  778. endoreg_db/views/video/task_status.py +49 -0
  779. endoreg_db/views/video/timeline.py +46 -0
  780. endoreg_db/views/video/video_analyze.py +52 -0
  781. endoreg_db/views/video/video_apply_mask.py +48 -0
  782. endoreg_db/views/video/video_correction.py +21 -0
  783. endoreg_db/views/video/video_download_processed.py +58 -0
  784. endoreg_db/views/video/video_examination_viewset.py +329 -0
  785. endoreg_db/views/video/video_media.py +158 -0
  786. endoreg_db/views/video/video_meta.py +29 -0
  787. endoreg_db/views/video/video_processing_history.py +24 -0
  788. endoreg_db/views/video/video_remove_frames.py +48 -0
  789. endoreg_db/views/video/video_stream.py +306 -0
  790. endoreg_db/views.py +0 -0
  791. endoreg_db-0.8.5.1.dist-info/METADATA +383 -0
  792. endoreg_db-0.8.5.1.dist-info/RECORD +794 -0
  793. endoreg_db-0.8.5.1.dist-info/WHEEL +4 -0
  794. endoreg_db-0.8.5.1.dist-info/licenses/LICENSE +674 -0
@@ -0,0 +1,226 @@
1
+ from rest_framework import status
2
+ from rest_framework.response import Response
3
+ from rest_framework.views import APIView
4
+ from django.db import transaction
5
+ from endoreg_db.models import LabelVideoSegment, VideoFile
6
+ from endoreg_db.utils.permissions import DEBUG_PERMISSIONS
7
+
8
+
9
+ class LabelVideoSegmentValidateView(APIView):
10
+ """
11
+ POST /api/label-video-segment/<int:segment_id>/validate/
12
+
13
+ Validiert ein einzelnes LabelVideoSegment und markiert es als verifiziert.
14
+ Dies wird verwendet, um vom Benutzer überprüfte Segment-Annotationen zu bestätigen.
15
+
16
+ Body (optional):
17
+ {
18
+ "is_validated": true, // optional, default true
19
+ "notes": "..." // optional, Validierungsnotizen
20
+ }
21
+ """
22
+ permission_classes = DEBUG_PERMISSIONS
23
+
24
+ @transaction.atomic
25
+ def post(self, request, segment_id: int):
26
+ try:
27
+ # Segment abrufen
28
+ segment = LabelVideoSegment.objects.select_related('state', 'video_file', 'label').get(pk=segment_id)
29
+
30
+ # Validierungsstatus aus Request (default: True)
31
+ is_validated = request.data.get('is_validated', True)
32
+ notes = request.data.get('notes', '')
33
+
34
+ # State-Objekt abrufen oder erstellen
35
+ if not hasattr(segment, 'state') or segment.state is None:
36
+ # State muss existieren - wenn nicht, könnte ein Model-Problem vorliegen
37
+ return Response({
38
+ "error": "Segment has no state object. Cannot validate."
39
+ }, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
40
+
41
+ # State aktualisieren
42
+ segment.state.is_validated = is_validated
43
+ if notes:
44
+ # Falls ein notes-Feld existiert
45
+ if hasattr(segment.state, 'validation_notes'):
46
+ segment.state.validation_notes = notes
47
+ segment.state.save()
48
+
49
+ return Response({
50
+ "message": f"Segment {segment_id} validation status updated.",
51
+ "segment_id": segment_id,
52
+ "is_validated": is_validated,
53
+ "label": segment.label.name if segment.label else None,
54
+ "video_id": segment.video_file.id if segment.video_file else None,
55
+ "start_frame": segment.start_frame_number,
56
+ "end_frame": segment.end_frame_number
57
+ }, status=status.HTTP_200_OK)
58
+
59
+ except LabelVideoSegment.DoesNotExist:
60
+ return Response({
61
+ "error": f"Segment {segment_id} not found."
62
+ }, status=status.HTTP_404_NOT_FOUND)
63
+ except Exception as e:
64
+ import logging
65
+ logger = logging.getLogger(__name__)
66
+ logger.error(f"Error validating segment {segment_id}: {e}")
67
+ return Response({
68
+ "error": f"Validation failed: {str(e)}"
69
+ }, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
70
+
71
+
72
+ class BulkSegmentValidateView(APIView):
73
+ """
74
+ POST /api/label-video-segments/validate-bulk/
75
+
76
+ Validiert mehrere LabelVideoSegments gleichzeitig.
77
+ Nützlich für Batch-Validierung nach Review.
78
+
79
+ Body:
80
+ {
81
+ "segment_ids": [1, 2, 3, ...],
82
+ "is_validated": true, // optional, default true
83
+ "notes": "..." // optional, gilt für alle Segmente
84
+ }
85
+ """
86
+ permission_classes = DEBUG_PERMISSIONS
87
+
88
+ @transaction.atomic
89
+ def post(self, request):
90
+ segment_ids = request.data.get('segment_ids', [])
91
+ is_validated = request.data.get('is_validated', True)
92
+ notes = request.data.get('notes', '')
93
+
94
+ if not segment_ids:
95
+ return Response({
96
+ "error": "segment_ids is required"
97
+ }, status=status.HTTP_400_BAD_REQUEST)
98
+
99
+ try:
100
+ # Alle Segmente abrufen
101
+ segments = LabelVideoSegment.objects.filter(pk__in=segment_ids).select_related('state')
102
+
103
+ if not segments.exists():
104
+ return Response({
105
+ "error": "No segments found with provided IDs"
106
+ }, status=status.HTTP_404_NOT_FOUND)
107
+
108
+ updated_count = 0
109
+ failed_ids = []
110
+
111
+ for segment in segments:
112
+ try:
113
+ if segment.state:
114
+ segment.state.is_validated = is_validated
115
+ if notes and hasattr(segment.state, 'validation_notes'):
116
+ segment.state.validation_notes = notes
117
+ segment.state.save()
118
+ updated_count += 1
119
+ else:
120
+ failed_ids.append(segment.id)
121
+ except Exception as e:
122
+ import logging
123
+ logger = logging.getLogger(__name__)
124
+ logger.error(f"Error validating segment {segment.id}: {e}")
125
+ failed_ids.append(segment.id)
126
+
127
+ response_data = {
128
+ "message": f"Bulk validation completed. {updated_count} segments updated.",
129
+ "updated_count": updated_count,
130
+ "requested_count": len(segment_ids),
131
+ "is_validated": is_validated
132
+ }
133
+
134
+ if failed_ids:
135
+ response_data["failed_ids"] = failed_ids
136
+ response_data["warning"] = f"{len(failed_ids)} segments could not be validated"
137
+
138
+ return Response(response_data, status=status.HTTP_200_OK)
139
+
140
+ except Exception as e:
141
+ import logging
142
+ logger = logging.getLogger(__name__)
143
+ logger.error(f"Error in bulk validation: {e}")
144
+ return Response({
145
+ "error": f"Bulk validation failed: {str(e)}"
146
+ }, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
147
+
148
+
149
+ class VideoSegmentValidationCompleteView(APIView):
150
+ """
151
+ POST /api/videos/<int:video_id>/segments/validate-complete/
152
+
153
+ Markiert alle Segmente eines Videos als validiert.
154
+ Nützlich nach vollständiger Review eines Videos.
155
+
156
+ Body (optional):
157
+ {
158
+ "label_name": "...", // optional, nur Segmente mit diesem Label validieren
159
+ "notes": "..." // optional
160
+ }
161
+ """
162
+ permission_classes = DEBUG_PERMISSIONS
163
+
164
+ @transaction.atomic
165
+ def post(self, request, video_id: int):
166
+ try:
167
+ # Video abrufen
168
+ video = VideoFile.objects.get(pk=video_id)
169
+
170
+ label_name = request.data.get('label_name')
171
+ notes = request.data.get('notes', '')
172
+
173
+ # Segmente filtern
174
+ segments_query = LabelVideoSegment.objects.filter(video_file=video).select_related('state', 'label')
175
+
176
+ if label_name:
177
+ segments_query = segments_query.filter(label__name=label_name)
178
+
179
+ segments = segments_query.all()
180
+
181
+ if not segments.exists():
182
+ return Response({
183
+ "message": "No segments found to validate",
184
+ "video_id": video_id,
185
+ "updated_count": 0
186
+ }, status=status.HTTP_200_OK)
187
+
188
+ updated_count = 0
189
+ failed_count = 0
190
+
191
+ for segment in segments:
192
+ try:
193
+ if segment.state:
194
+ segment.state.is_validated = True
195
+ if notes and hasattr(segment.state, 'validation_notes'):
196
+ segment.state.validation_notes = notes
197
+ segment.state.save()
198
+ updated_count += 1
199
+ else:
200
+ failed_count += 1
201
+ except Exception as e:
202
+ import logging
203
+ logger = logging.getLogger(__name__)
204
+ logger.error(f"Error validating segment {segment.id}: {e}")
205
+ failed_count += 1
206
+
207
+ return Response({
208
+ "message": f"Video segment validation completed for video {video_id}",
209
+ "video_id": video_id,
210
+ "total_segments": len(segments),
211
+ "updated_count": updated_count,
212
+ "failed_count": failed_count,
213
+ "label_filter": label_name
214
+ }, status=status.HTTP_200_OK)
215
+
216
+ except VideoFile.DoesNotExist:
217
+ return Response({
218
+ "error": f"Video {video_id} not found"
219
+ }, status=status.HTTP_404_NOT_FOUND)
220
+ except Exception as e:
221
+ import logging
222
+ logger = logging.getLogger(__name__)
223
+ logger.error(f"Error completing validation for video {video_id}: {e}")
224
+ return Response({
225
+ "error": f"Validation completion failed: {str(e)}"
226
+ }, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
@@ -0,0 +1,45 @@
1
+ # Media Management Views (Phase 1.2)
2
+
3
+ from .video_media import VideoMediaView
4
+ from .pdf_media import PdfMediaView
5
+ from ..video.reimport import VideoReimportView
6
+ from ..pdf.reimport import PdfReimportView
7
+ from .segments import video_segments_by_pk
8
+ from .video_segments import (
9
+ video_segments_collection,
10
+ video_segments_by_video,
11
+ video_segment_detail,
12
+ video_segments_stats,
13
+ video_segment_validate,
14
+ video_segments_validate_bulk,
15
+ video_segments_validation_status,
16
+ )
17
+ from .sensitive_metadata import (
18
+ video_sensitive_metadata,
19
+ video_sensitive_metadata_verify,
20
+ pdf_sensitive_metadata,
21
+ pdf_sensitive_metadata_verify,
22
+ sensitive_metadata_list,
23
+ pdf_sensitive_metadata_list,
24
+ )
25
+
26
+ __all__ = [
27
+ 'VideoMediaView',
28
+ 'PdfMediaView',
29
+ 'VideoReimportView',
30
+ 'PdfReimportView',
31
+ 'video_segments_by_pk',
32
+ 'video_segments_collection',
33
+ 'video_segments_by_video',
34
+ 'video_segment_detail',
35
+ 'video_segments_stats',
36
+ 'video_segment_validate',
37
+ 'video_segments_validate_bulk',
38
+ 'video_segments_validation_status',
39
+ 'video_sensitive_metadata',
40
+ 'video_sensitive_metadata_verify',
41
+ 'pdf_sensitive_metadata',
42
+ 'pdf_sensitive_metadata_verify',
43
+ 'sensitive_metadata_list',
44
+ 'pdf_sensitive_metadata_list',
45
+ ]
@@ -0,0 +1,386 @@
1
+ """
2
+ PDF Media Management View (Phase 1.2)
3
+
4
+ Provides standardized REST API for PDF files including listing, detail retrieval,
5
+ and streaming for the media management system.
6
+
7
+ This is separate from the existing pdf.PDFMediaView which handles legacy workflows.
8
+ """
9
+
10
+ import logging
11
+ import os
12
+ from django.http import Http404, FileResponse
13
+ from rest_framework import status
14
+ from rest_framework.response import Response
15
+ from rest_framework.views import APIView
16
+ from django.db.models import Q
17
+
18
+ from endoreg_db.models import RawPdfFile
19
+ from endoreg_db.utils.permissions import EnvironmentAwarePermission
20
+
21
+ logger = logging.getLogger(__name__)
22
+
23
+
24
+ class PdfMediaView(APIView):
25
+ """
26
+ PDF Media Management API for CRUD operations on PDF files.
27
+
28
+ Endpoints:
29
+ - GET /api/media/pdfs/ - List all PDFs with filtering
30
+ - GET /api/media/pdfs/{id}/ - Get PDF details
31
+ - GET /api/media/pdfs/{id}/stream/ - Stream PDF file (same as detail for PDFs)
32
+ - PATCH /api/media/pdfs/{id}/ - Update PDF metadata (future)
33
+ - DELETE /api/media/pdfs/{id}/ - Delete PDF (future)
34
+
35
+ Query Parameters:
36
+ - status: Filter by processing status (not_started, done, validated)
37
+ - search: Search in filename
38
+ - limit: Limit results (default: 50)
39
+ - offset: Pagination offset
40
+
41
+ Examples:
42
+ - GET /api/media/pdfs/?status=done&search=exam
43
+ - GET /api/media/pdfs/123/
44
+ - GET /api/media/pdfs/123/stream/
45
+
46
+ Phase 1.2 Implementation:
47
+ - List and detail views implemented
48
+ - PDF streaming functionality
49
+ - Filtering and search functionality
50
+ - Pagination support
51
+ - Error handling with proper HTTP status codes
52
+ """
53
+ permission_classes = [EnvironmentAwarePermission]
54
+
55
+ def get(self, request, pk=None):
56
+ """
57
+ Handle GET requests for PDF listing, detail retrieval, or streaming.
58
+
59
+ Args:
60
+ request: HTTP request object
61
+ pk: Optional PDF ID for detail view or streaming
62
+
63
+ Returns:
64
+ Response or FileResponse: JSON response with PDF data or PDF file stream
65
+
66
+ Raises:
67
+ Http404: If specific PDF not found
68
+ """
69
+ if pk is not None:
70
+ # Check if this is a streaming request
71
+ if request.path.endswith('/stream/'):
72
+ return self._stream_pdf(pk)
73
+ else:
74
+ # Detail view
75
+ return self._get_pdf_detail(pk)
76
+ else:
77
+ # List view
78
+ return self._list_pdfs(request)
79
+
80
+ def _get_pdf_detail(self, pk):
81
+ """
82
+ Get detailed information for a specific PDF.
83
+
84
+ Args:
85
+ pk: PDF primary key
86
+
87
+ Returns:
88
+ Response: JSON response with PDF details
89
+
90
+ Raises:
91
+ Http404: If PDF not found
92
+ """
93
+ try:
94
+ # Validate pdf_id is numeric
95
+ try:
96
+ pdf_id_int = int(pk)
97
+ except (ValueError, TypeError):
98
+ raise Http404("Invalid PDF ID format")
99
+
100
+ # Fetch PDF with related data
101
+ pdf = RawPdfFile.objects.select_related('sensitive_meta').get(pk=pdf_id_int)
102
+
103
+ # Build PDF details
104
+ pdf_data = {
105
+ "id": pdf.id,
106
+ "filename": getattr(pdf.file, 'name', 'Unknown'),
107
+ "file_size": getattr(pdf.file, 'size', 0),
108
+ "pdf_hash": pdf.pdf_hash,
109
+ "uploaded_at": pdf.uploaded_at.isoformat() if hasattr(pdf, 'uploaded_at') else None,
110
+ "anonymized_text": pdf.anonymized_text,
111
+ "has_anonymized_text": bool(pdf.anonymized_text and pdf.anonymized_text.strip()),
112
+ "is_validated": getattr(pdf.sensitive_meta, 'is_verified', False) if pdf.sensitive_meta else False,
113
+ "stream_url": self.request.build_absolute_uri(f"/api/media/pdfs/{pdf.id}/stream/"),
114
+ }
115
+
116
+ # Add patient metadata if available
117
+ if pdf.sensitive_meta:
118
+ pdf_data.update({
119
+ "patient_first_name": pdf.sensitive_meta.patient_first_name,
120
+ "patient_last_name": pdf.sensitive_meta.patient_last_name,
121
+ "patient_dob": pdf.sensitive_meta.patient_dob.strftime("%d.%m.%Y") if pdf.sensitive_meta.patient_dob else None,
122
+ "examination_date": pdf.sensitive_meta.examination_date.strftime("%d.%m.%Y") if pdf.sensitive_meta.examination_date else None,
123
+ })
124
+
125
+ return Response(pdf_data)
126
+
127
+ except RawPdfFile.DoesNotExist:
128
+ raise Http404(f"PDF with ID {pk} not found")
129
+
130
+ except Exception as e:
131
+ logger.error(f"Unexpected error in PDF detail view for ID {pk}: {str(e)}")
132
+ return Response(
133
+ {"error": "Failed to retrieve PDF details"},
134
+ status=status.HTTP_500_INTERNAL_SERVER_ERROR
135
+ )
136
+
137
+ def _stream_pdf(self, pk):
138
+ """
139
+ Stream PDF file content for viewing/download.
140
+
141
+ Args:
142
+ pk: PDF primary key
143
+
144
+ Returns:
145
+ FileResponse: PDF file stream
146
+
147
+ Raises:
148
+ Http404: If PDF not found or file cannot be accessed
149
+ """
150
+ try:
151
+ # Validate pdf_id is numeric
152
+ try:
153
+ pdf_id_int = int(pk)
154
+ except (ValueError, TypeError):
155
+ raise Http404("Invalid PDF ID format")
156
+
157
+ # Fetch PDF
158
+ pdf = RawPdfFile.objects.get(pk=pdf_id_int)
159
+
160
+ # Check if file exists
161
+ if not pdf.file or not pdf.file.name:
162
+ raise Http404("PDF file not found")
163
+
164
+ try:
165
+ # Open file for streaming
166
+ file_path = pdf.file.path
167
+ if not os.path.exists(file_path):
168
+ raise Http404("PDF file does not exist on disk")
169
+
170
+ # Create file response
171
+ response = FileResponse(
172
+ open(file_path, 'rb'),
173
+ content_type='application/pdf',
174
+ as_attachment=False # View in browser, not download
175
+ )
176
+
177
+ # Set filename for browser
178
+ filename = os.path.basename(pdf.file.name)
179
+ response['Content-Disposition'] = f'inline; filename="{filename}"'
180
+
181
+ # CORS headers for frontend access
182
+ frontend_origin = os.environ.get('FRONTEND_ORIGIN', 'http://localhost:8000')
183
+ response['Access-Control-Allow-Origin'] = frontend_origin
184
+ response['Access-Control-Allow-Credentials'] = 'true'
185
+
186
+ return response
187
+
188
+ except (OSError, IOError) as e:
189
+ logger.error(f"File access error for PDF {pk}: {str(e)}")
190
+ raise Http404("PDF file cannot be accessed")
191
+
192
+ except RawPdfFile.DoesNotExist:
193
+ raise Http404(f"PDF with ID {pk} not found")
194
+
195
+ except Exception as e:
196
+ logger.error(f"Unexpected error in PDF streaming for ID {pk}: {str(e)}")
197
+ raise Http404("PDF file cannot be streamed")
198
+
199
+ def _list_pdfs(self, request):
200
+ """
201
+ List PDFs with filtering, search, and pagination.
202
+
203
+ Args:
204
+ request: HTTP request with query parameters
205
+
206
+ Returns:
207
+ Response: JSON response with paginated PDF list
208
+ """
209
+ try:
210
+ # Start with all PDFs
211
+ queryset = RawPdfFile.objects.select_related('sensitive_meta').all()
212
+
213
+ # Apply filters
214
+ queryset = self._apply_filters(queryset, request.query_params)
215
+
216
+ # Apply search
217
+ search = request.query_params.get('search', '').strip()
218
+ if search:
219
+ queryset = queryset.filter(
220
+ Q(file__icontains=search)
221
+ )
222
+
223
+ # Order by upload date (newest first) or id if no upload date
224
+ if hasattr(queryset.model, 'uploaded_at'):
225
+ queryset = queryset.order_by('-uploaded_at')
226
+ else:
227
+ queryset = queryset.order_by('-id')
228
+
229
+ # Apply pagination
230
+ limit = min(int(request.query_params.get('limit', 50)), 100)
231
+ offset = int(request.query_params.get('offset', 0))
232
+
233
+ total_count = queryset.count()
234
+ pdfs = queryset[offset:offset + limit]
235
+
236
+ # Serialize PDFs manually (no dedicated serializer yet)
237
+ results = []
238
+ for pdf in pdfs:
239
+ pdf_item = {
240
+ "id": pdf.id,
241
+ "filename": getattr(pdf.file, 'name', 'Unknown'),
242
+ "file_size": self._safe_get_file_size(pdf.file),
243
+ "pdf_hash": pdf.pdf_hash,
244
+ "has_anonymized_text": bool(pdf.anonymized_text and pdf.anonymized_text.strip()),
245
+ "is_validated": getattr(pdf.sensitive_meta, 'is_verified', False) if pdf.sensitive_meta else False,
246
+ "stream_url": request.build_absolute_uri(f"/api/media/pdfs/{pdf.id}/stream/"),
247
+ }
248
+
249
+ # Determine status based on anonymization and validation
250
+ if not pdf.anonymized_text or not pdf.anonymized_text.strip():
251
+ pdf_item["status"] = "not_started"
252
+ elif pdf.sensitive_meta and pdf.sensitive_meta.is_verified:
253
+ pdf_item["status"] = "validated"
254
+ else:
255
+ pdf_item["status"] = "done"
256
+
257
+ results.append(pdf_item)
258
+
259
+ return Response({
260
+ "count": total_count,
261
+ "next": self._get_next_url(request, offset, limit, total_count),
262
+ "previous": self._get_previous_url(request, offset, limit),
263
+ "results": results
264
+ })
265
+
266
+ except ValueError as e:
267
+ return Response(
268
+ {"error": f"Invalid query parameter: {str(e)}"},
269
+ status=status.HTTP_400_BAD_REQUEST
270
+ )
271
+
272
+ except Exception as e:
273
+ logger.error(f"Unexpected error in PDF list view: {str(e)}")
274
+ return Response(
275
+ {"error": "Failed to retrieve PDF list"},
276
+ status=status.HTTP_500_INTERNAL_SERVER_ERROR
277
+ )
278
+
279
+ def _safe_get_file_size(self, file_field):
280
+ """
281
+ Safely get file size without causing errors if file doesn't exist.
282
+
283
+ Args:
284
+ file_field: Django FileField
285
+
286
+ Returns:
287
+ int: File size in bytes, or 0 if file doesn't exist
288
+ """
289
+ if not file_field or not file_field.name:
290
+ return 0
291
+
292
+ try:
293
+ return file_field.size
294
+ except (OSError, IOError, ValueError):
295
+ # File doesn't exist on disk or is corrupted
296
+ return 0
297
+
298
+ def _apply_filters(self, queryset, query_params):
299
+ """
300
+ Apply status and other filters to PDF queryset.
301
+
302
+ Args:
303
+ queryset: Base queryset to filter
304
+ query_params: Request query parameters
305
+
306
+ Returns:
307
+ QuerySet: Filtered queryset
308
+ """
309
+ status_filter = query_params.get('status', '').strip().lower()
310
+
311
+ if status_filter:
312
+ if status_filter == 'not_started':
313
+ # PDFs without anonymized text
314
+ queryset = queryset.filter(
315
+ Q(anonymized_text__isnull=True) | Q(anonymized_text__exact='')
316
+ )
317
+ elif status_filter == 'done':
318
+ # PDFs with anonymized text but not validated
319
+ queryset = queryset.filter(
320
+ ~Q(anonymized_text__isnull=True),
321
+ ~Q(anonymized_text__exact=''),
322
+ Q(sensitive_meta__is_verified=False) | Q(sensitive_meta__isnull=True)
323
+ )
324
+ elif status_filter == 'validated':
325
+ # PDFs with anonymized text and validated
326
+ queryset = queryset.filter(
327
+ ~Q(anonymized_text__isnull=True),
328
+ ~Q(anonymized_text__exact=''),
329
+ sensitive_meta__is_verified=True
330
+ )
331
+
332
+ return queryset
333
+
334
+ def _get_next_url(self, request, offset, limit, total_count):
335
+ """Generate next page URL for pagination."""
336
+ if offset + limit >= total_count:
337
+ return None
338
+
339
+ next_offset = offset + limit
340
+ return self._build_paginated_url(request, next_offset, limit)
341
+
342
+ def _get_previous_url(self, request, offset, limit):
343
+ """Generate previous page URL for pagination."""
344
+ if offset <= 0:
345
+ return None
346
+
347
+ prev_offset = max(0, offset - limit)
348
+ return self._build_paginated_url(request, prev_offset, limit)
349
+
350
+ def _build_paginated_url(self, request, offset, limit):
351
+ """Build URL with pagination parameters."""
352
+ params = request.query_params.copy()
353
+ params['offset'] = offset
354
+ params['limit'] = limit
355
+
356
+ base_url = request.build_absolute_uri(request.path)
357
+ if params:
358
+ return f"{base_url}?{params.urlencode()}"
359
+ return base_url
360
+
361
+ # Future implementation placeholders
362
+ def patch(self, request, pk):
363
+ """
364
+ Update PDF metadata (Phase 1.2+ future enhancement).
365
+
366
+ Currently returns 501 Not Implemented.
367
+ """
368
+ return Response(
369
+ {"error": "PDF metadata updates not yet implemented"},
370
+ status=status.HTTP_501_NOT_IMPLEMENTED
371
+ )
372
+
373
+ def delete(self, request, pk):
374
+ """
375
+ Delete PDF file (Phase 1.2+ future enhancement).
376
+
377
+ Currently returns 501 Not Implemented.
378
+ Use /api/media-management/force-remove/{id}/ instead.
379
+ """
380
+ return Response(
381
+ {
382
+ "error": "PDF deletion not yet implemented",
383
+ "alternative": f"Use DELETE /api/media-management/force-remove/{pk}/ instead"
384
+ },
385
+ status=status.HTTP_501_NOT_IMPLEMENTED
386
+ )