endoreg-db 0.8.9.32__py3-none-any.whl
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- endoreg_db/__init__.py +0 -0
- endoreg_db/_version.py +34 -0
- endoreg_db/admin.py +97 -0
- endoreg_db/api/serializers/finding_descriptions.py +0 -0
- endoreg_db/api/views/finding_descriptions.py +0 -0
- endoreg_db/api_urls.py +4 -0
- endoreg_db/apps.py +17 -0
- endoreg_db/assets/dummy_model.ckpt +1 -0
- endoreg_db/authz/auth.py +78 -0
- endoreg_db/authz/backends.py +168 -0
- endoreg_db/authz/management/commands/list_routes.py +20 -0
- endoreg_db/authz/middleware.py +84 -0
- endoreg_db/authz/permissions.py +138 -0
- endoreg_db/authz/policy.py +224 -0
- endoreg_db/authz/settings.py +64 -0
- endoreg_db/authz/views_auth.py +70 -0
- endoreg_db/codemods/readme.md +88 -0
- endoreg_db/codemods/rename_datetime_fields.py +99 -0
- endoreg_db/config/__init__.py +0 -0
- endoreg_db/config/env.py +106 -0
- endoreg_db/config/settings/__init__.py +6 -0
- endoreg_db/config/settings/base.py +148 -0
- endoreg_db/config/settings/case_gen.py +32 -0
- endoreg_db/config/settings/dev.py +108 -0
- endoreg_db/config/settings/keycloak.py +177 -0
- endoreg_db/config/settings/prod.py +66 -0
- endoreg_db/config/settings/test.py +72 -0
- endoreg_db/data/__init__.py +135 -0
- endoreg_db/data/ai_model/data.yaml +7 -0
- endoreg_db/data/ai_model_label/label/data.yaml +88 -0
- endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
- endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
- endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
- endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
- endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
- endoreg_db/data/ai_model_type/data.yaml +7 -0
- endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
- endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
- endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
- endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
- endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
- endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
- endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
- endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
- endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
- endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
- endoreg_db/data/case_template/rule_value/.init +0 -0
- endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
- endoreg_db/data/case_template/template/base.yaml +8 -0
- endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
- endoreg_db/data/case_template/tmp/_rule_value +13 -0
- endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
- endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
- endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
- endoreg_db/data/center/data.yaml +99 -0
- endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
- endoreg_db/data/center_shift/ukw.yaml +9 -0
- endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
- endoreg_db/data/contraindication/bleeding.yaml +11 -0
- endoreg_db/data/db_summary.csv +58 -0
- endoreg_db/data/db_summary.xlsx +0 -0
- endoreg_db/data/disease/cardiovascular.yaml +37 -0
- endoreg_db/data/disease/hepatology.yaml +5 -0
- endoreg_db/data/disease/misc.yaml +5 -0
- endoreg_db/data/disease/renal.yaml +5 -0
- endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
- endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
- endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
- endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
- endoreg_db/data/distribution/date/patient.yaml +7 -0
- endoreg_db/data/distribution/multiple_categorical/.init +0 -0
- endoreg_db/data/distribution/numeric/data.yaml +14 -0
- endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
- endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
- endoreg_db/data/endoscope/data.yaml +93 -0
- endoreg_db/data/endoscope_type/data.yaml +11 -0
- endoreg_db/data/endoscopy_processor/data.yaml +50 -0
- endoreg_db/data/event/cardiology.yaml +15 -0
- endoreg_db/data/event/neurology.yaml +14 -0
- endoreg_db/data/event/surgery.yaml +13 -0
- endoreg_db/data/event/thrombembolism.yaml +20 -0
- endoreg_db/data/event_classification/data.yaml +4 -0
- endoreg_db/data/event_classification_choice/data.yaml +9 -0
- endoreg_db/data/examination/examinations/data.yaml +172 -0
- endoreg_db/data/examination/time/data.yaml +48 -0
- endoreg_db/data/examination/time-type/data.yaml +5 -0
- endoreg_db/data/examination/type/data.yaml +17 -0
- endoreg_db/data/examination_indication/endoscopy.yaml +359 -0
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +90 -0
- endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +97 -0
- endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
- endoreg_db/data/finding/00_generic.yaml +35 -0
- endoreg_db/data/finding/00_generic_complication.yaml +9 -0
- endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
- endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
- endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
- endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
- endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
- endoreg_db/data/finding_classification/00_generic.yaml +44 -0
- endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
- endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
- endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
- endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
- endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
- endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
- endoreg_db/data/finding_classification_choice/00_generic.yaml +15 -0
- endoreg_db/data/finding_classification_choice/00_generic_baseline.yaml +23 -0
- endoreg_db/data/finding_classification_choice/00_generic_complication.yaml +15 -0
- endoreg_db/data/finding_classification_choice/00_generic_histology.yaml +21 -0
- endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_bowel_preparation.yaml +49 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_generic.yaml +19 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_histology.yaml +20 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_location.yaml +248 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_morphology.yaml +75 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
- endoreg_db/data/finding_classification_type/00_generic.yaml +53 -0
- endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
- endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
- endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
- endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
- endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
- endoreg_db/data/finding_type/data.yaml +39 -0
- endoreg_db/data/gender/data.yaml +42 -0
- endoreg_db/data/information_source/annotation.yaml +6 -0
- endoreg_db/data/information_source/data.yaml +30 -0
- endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
- endoreg_db/data/information_source/medication.yaml +6 -0
- endoreg_db/data/information_source/prediction.yaml +7 -0
- endoreg_db/data/information_source_type/data.yaml +8 -0
- endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
- endoreg_db/data/lab_value/coagulation.yaml +54 -0
- endoreg_db/data/lab_value/electrolytes.yaml +228 -0
- endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
- endoreg_db/data/lab_value/hematology.yaml +184 -0
- endoreg_db/data/lab_value/hormones.yaml +59 -0
- endoreg_db/data/lab_value/lipids.yaml +53 -0
- endoreg_db/data/lab_value/misc.yaml +76 -0
- endoreg_db/data/lab_value/renal_function.yaml +12 -0
- endoreg_db/data/log_type/data.yaml +57 -0
- endoreg_db/data/lx_client_tag/base.yaml +54 -0
- endoreg_db/data/lx_client_type/base.yaml +30 -0
- endoreg_db/data/lx_permission/base.yaml +24 -0
- endoreg_db/data/lx_permission/endoreg.yaml +52 -0
- endoreg_db/data/material/material.yaml +91 -0
- endoreg_db/data/medication/anticoagulation.yaml +65 -0
- endoreg_db/data/medication/tah.yaml +70 -0
- endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
- endoreg_db/data/medication_indication_type/data.yaml +11 -0
- endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
- endoreg_db/data/medication_intake_time/base.yaml +31 -0
- endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
- endoreg_db/data/medication_schedule/ass.yaml +12 -0
- endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
- endoreg_db/data/names_first/first_names.yaml +54 -0
- endoreg_db/data/names_last/last_names.yaml +51 -0
- endoreg_db/data/network_device/data.yaml +59 -0
- endoreg_db/data/network_device_type/data.yaml +12 -0
- endoreg_db/data/organ/data.yaml +29 -0
- endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
- endoreg_db/data/pdf_type/data.yaml +46 -0
- endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
- endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
- endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
- endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
- endoreg_db/data/profession/data.yaml +70 -0
- endoreg_db/data/qualification/endoscopy.yaml +36 -0
- endoreg_db/data/qualification/m2.yaml +39 -0
- endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
- endoreg_db/data/qualification/sonography.yaml +36 -0
- endoreg_db/data/qualification_type/base.yaml +29 -0
- endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
- endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
- endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
- endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
- endoreg_db/data/requirement/01_patient_data.yaml +93 -0
- endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
- endoreg_db/data/requirement/old/colonoscopy_baseline_austria.yaml +45 -0
- endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
- endoreg_db/data/requirement/old/disease_cardiovascular.yaml +79 -0
- endoreg_db/data/requirement/old/disease_classification_choice_cardiovascular.yaml +41 -0
- endoreg_db/data/requirement/old/disease_hepatology.yaml +12 -0
- endoreg_db/data/requirement/old/disease_misc.yaml +12 -0
- endoreg_db/data/requirement/old/disease_renal.yaml +96 -0
- endoreg_db/data/requirement/old/endoscopy_bleeding_risk.yaml +59 -0
- endoreg_db/data/requirement/old/event_cardiology.yaml +251 -0
- endoreg_db/data/requirement/old/event_requirements.yaml +145 -0
- endoreg_db/data/requirement/old/finding_colon_polyp.yaml +50 -0
- endoreg_db/data/requirement/old/gender.yaml +0 -0
- endoreg_db/data/requirement/old/lab_value.yaml +441 -0
- endoreg_db/data/requirement/old/medication.yaml +93 -0
- endoreg_db/data/requirement_operator/_old/age.yaml +13 -0
- endoreg_db/data/requirement_operator/_old/lab_operators.yaml +129 -0
- endoreg_db/data/requirement_operator/_old/model_operators.yaml +96 -0
- endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +65 -0
- endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
- endoreg_db/data/requirement_set/02_endoscopy_bleeding_risk.yaml +46 -0
- endoreg_db/data/requirement_set/90_coloreg.yaml +190 -0
- endoreg_db/data/requirement_set/_old_ +109 -0
- endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
- endoreg_db/data/requirement_set_type/data.yaml +41 -0
- endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
- endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
- endoreg_db/data/risk/bleeding.yaml +26 -0
- endoreg_db/data/risk/thrombosis.yaml +37 -0
- endoreg_db/data/risk_type/data.yaml +27 -0
- endoreg_db/data/setup_config.yaml +38 -0
- endoreg_db/data/shift/endoscopy.yaml +21 -0
- endoreg_db/data/shift/m2.yaml +0 -0
- endoreg_db/data/shift_type/base.yaml +35 -0
- endoreg_db/data/tag/requirement_set_tags.yaml +32 -0
- endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
- endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
- endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
- endoreg_db/data/unit/concentration.yaml +115 -0
- endoreg_db/data/unit/data.yaml +17 -0
- endoreg_db/data/unit/length.yaml +31 -0
- endoreg_db/data/unit/misc.yaml +20 -0
- endoreg_db/data/unit/rate.yaml +6 -0
- endoreg_db/data/unit/time.yaml +48 -0
- endoreg_db/data/unit/volume.yaml +35 -0
- endoreg_db/data/unit/weight.yaml +38 -0
- endoreg_db/data/waste/data.yaml +12 -0
- endoreg_db/exceptions.py +24 -0
- endoreg_db/export/frames/export.py +6 -0
- endoreg_db/export/frames/export_frames_with_labels.py +616 -0
- endoreg_db/factories/__init__.py +0 -0
- endoreg_db/forms/__init__.py +4 -0
- endoreg_db/forms/examination_form.py +12 -0
- endoreg_db/forms/patient_finding_intervention_form.py +40 -0
- endoreg_db/forms/patient_form.py +23 -0
- endoreg_db/forms/questionnaires/__init__.py +1 -0
- endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
- endoreg_db/forms/settings/__init__.py +11 -0
- endoreg_db/forms/unit.py +7 -0
- endoreg_db/helpers/__init__.py +0 -0
- endoreg_db/helpers/count_db.py +48 -0
- endoreg_db/helpers/data_loader.py +280 -0
- endoreg_db/helpers/default_objects.py +414 -0
- endoreg_db/helpers/download_segmentation_model.py +32 -0
- endoreg_db/helpers/interact.py +1 -0
- endoreg_db/helpers/test_video_helper.py +127 -0
- endoreg_db/import_files/__init__.py +27 -0
- endoreg_db/import_files/context/__init__.py +7 -0
- endoreg_db/import_files/context/default_sensitive_meta.py +83 -0
- endoreg_db/import_files/context/ensure_center.py +17 -0
- endoreg_db/import_files/context/file_lock.py +66 -0
- endoreg_db/import_files/context/import_context.py +42 -0
- endoreg_db/import_files/context/validate_directories.py +57 -0
- endoreg_db/import_files/file_storage/__init__.py +15 -0
- endoreg_db/import_files/file_storage/create_report_file.py +99 -0
- endoreg_db/import_files/file_storage/create_video_file.py +104 -0
- endoreg_db/import_files/file_storage/sensitive_meta_storage.py +42 -0
- endoreg_db/import_files/file_storage/state_management.py +463 -0
- endoreg_db/import_files/file_storage/storage.py +42 -0
- endoreg_db/import_files/import_service.md +26 -0
- endoreg_db/import_files/processing/__init__.py +11 -0
- endoreg_db/import_files/processing/report_processing/report_anonymization.py +99 -0
- endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
- endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
- endoreg_db/import_files/pseudonymization/__init__.py +0 -0
- endoreg_db/import_files/pseudonymization/fake.py +52 -0
- endoreg_db/import_files/pseudonymization/k_anonymity.py +181 -0
- endoreg_db/import_files/pseudonymization/k_pseudonymity.py +139 -0
- endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
- endoreg_db/import_files/report_import_service.py +147 -0
- endoreg_db/import_files/video_import_service.py +154 -0
- endoreg_db/logger_conf.py +156 -0
- endoreg_db/management/__init__.py +1 -0
- endoreg_db/management/commands/__init__.py +1 -0
- endoreg_db/management/commands/anonymize_video.py +0 -0
- endoreg_db/management/commands/check_auth.py +132 -0
- endoreg_db/management/commands/create_model_meta_from_huggingface.py +177 -0
- endoreg_db/management/commands/create_multilabel_model_meta.py +419 -0
- endoreg_db/management/commands/export_frame_annot.py +196 -0
- endoreg_db/management/commands/fix_missing_patient_data.py +206 -0
- endoreg_db/management/commands/fix_video_paths.py +186 -0
- endoreg_db/management/commands/import_report.py +361 -0
- endoreg_db/management/commands/list_routes.py +20 -0
- endoreg_db/management/commands/load_ai_model_data.py +83 -0
- endoreg_db/management/commands/load_ai_model_label_data.py +60 -0
- endoreg_db/management/commands/load_base_db_data.py +63 -0
- endoreg_db/management/commands/load_center_data.py +68 -0
- endoreg_db/management/commands/load_contraindication_data.py +39 -0
- endoreg_db/management/commands/load_disease_classification_choices_data.py +38 -0
- endoreg_db/management/commands/load_disease_classification_data.py +38 -0
- endoreg_db/management/commands/load_disease_data.py +59 -0
- endoreg_db/management/commands/load_distribution_data.py +63 -0
- endoreg_db/management/commands/load_endoscope_data.py +58 -0
- endoreg_db/management/commands/load_event_data.py +39 -0
- endoreg_db/management/commands/load_examination_data.py +78 -0
- endoreg_db/management/commands/load_examination_indication_data.py +85 -0
- endoreg_db/management/commands/load_finding_data.py +115 -0
- endoreg_db/management/commands/load_gender_data.py +37 -0
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +142 -0
- endoreg_db/management/commands/load_information_source.py +46 -0
- endoreg_db/management/commands/load_lab_value_data.py +52 -0
- endoreg_db/management/commands/load_legacy_data.py +303 -0
- endoreg_db/management/commands/load_medication_data.py +104 -0
- endoreg_db/management/commands/load_name_data.py +36 -0
- endoreg_db/management/commands/load_organ_data.py +39 -0
- endoreg_db/management/commands/load_pdf_type_data.py +58 -0
- endoreg_db/management/commands/load_profession_data.py +40 -0
- endoreg_db/management/commands/load_qualification_data.py +56 -0
- endoreg_db/management/commands/load_report_reader_flag_data.py +40 -0
- endoreg_db/management/commands/load_requirement_data.py +207 -0
- endoreg_db/management/commands/load_requirement_set_tags.py +95 -0
- endoreg_db/management/commands/load_risk_data.py +57 -0
- endoreg_db/management/commands/load_shift_data.py +57 -0
- endoreg_db/management/commands/load_tag_data.py +54 -0
- endoreg_db/management/commands/load_unit_data.py +40 -0
- endoreg_db/management/commands/load_user_groups.py +26 -0
- endoreg_db/management/commands/model_input.py +169 -0
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- endoreg_db/utils/check_video_files.py +175 -0
- endoreg_db/utils/cropping.py +30 -0
- endoreg_db/utils/dataloader.py +285 -0
- endoreg_db/utils/dates.py +59 -0
- endoreg_db/utils/defaults/set_default_center.py +33 -0
- endoreg_db/utils/env.py +37 -0
- endoreg_db/utils/extract_specific_frames.py +87 -0
- endoreg_db/utils/file_operations.py +70 -0
- endoreg_db/utils/fix_video_path_direct.py +157 -0
- endoreg_db/utils/frame_anonymization_utils.py +463 -0
- endoreg_db/utils/hashs.py +138 -0
- endoreg_db/utils/links/__init__.py +0 -0
- endoreg_db/utils/links/requirement_link.py +237 -0
- endoreg_db/utils/mime_types.py +0 -0
- endoreg_db/utils/names.py +82 -0
- endoreg_db/utils/ocr.py +195 -0
- endoreg_db/utils/operation_log.py +87 -0
- endoreg_db/utils/parse_and_generate_yaml.py +45 -0
- endoreg_db/utils/paths.py +159 -0
- endoreg_db/utils/permissions.py +160 -0
- endoreg_db/utils/pipelines/Readme.md +235 -0
- endoreg_db/utils/pipelines/__init__.py +0 -0
- endoreg_db/utils/pipelines/process_video_dir.py +144 -0
- endoreg_db/utils/product/__init__.py +0 -0
- endoreg_db/utils/product/sum_emissions.py +22 -0
- endoreg_db/utils/product/sum_weights.py +20 -0
- endoreg_db/utils/pydantic_models/__init__.py +5 -0
- endoreg_db/utils/pydantic_models/db_config.py +57 -0
- endoreg_db/utils/requirement_helpers.py +0 -0
- endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
- endoreg_db/utils/requirement_operator_logic/_old/lab_value_operators.py +678 -0
- endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +842 -0
- endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +114 -0
- endoreg_db/utils/setup_config.py +196 -0
- endoreg_db/utils/storage.py +117 -0
- endoreg_db/utils/translation.py +31 -0
- endoreg_db/utils/uuid.py +5 -0
- endoreg_db/utils/validate_endo_roi.py +33 -0
- endoreg_db/utils/validate_subcategory_dict.py +93 -0
- endoreg_db/utils/validate_video_detailed.py +415 -0
- endoreg_db/utils/video/__init__.py +30 -0
- endoreg_db/utils/video/extract_frames.py +100 -0
- endoreg_db/utils/video/ffmpeg_wrapper.py +996 -0
- endoreg_db/utils/video/names.py +47 -0
- endoreg_db/utils/video/streaming_processor.py +386 -0
- endoreg_db/utils/video/video_splitter.py +105 -0
- endoreg_db/versioning.md +79 -0
- endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +247 -0
- endoreg_db/views/__init__.py +157 -0
- endoreg_db/views/anonymization/__init__.py +31 -0
- endoreg_db/views/anonymization/media_management.py +486 -0
- endoreg_db/views/anonymization/overview.py +307 -0
- endoreg_db/views/anonymization/validate.py +310 -0
- endoreg_db/views/auth/__init__.py +13 -0
- endoreg_db/views/auth/keycloak.py +146 -0
- endoreg_db/views/examination/__init__.py +30 -0
- endoreg_db/views/examination/examination.py +37 -0
- endoreg_db/views/examination/examination_manifest_cache.py +26 -0
- endoreg_db/views/examination/get_finding_classification_choices.py +62 -0
- endoreg_db/views/examination/get_finding_classifications.py +38 -0
- endoreg_db/views/examination/get_findings.py +39 -0
- endoreg_db/views/examination/get_instruments.py +19 -0
- endoreg_db/views/examination/get_interventions.py +14 -0
- endoreg_db/views/finding/__init__.py +9 -0
- endoreg_db/views/finding/finding.py +116 -0
- endoreg_db/views/finding/get_classifications.py +14 -0
- endoreg_db/views/finding/get_interventions.py +17 -0
- endoreg_db/views/finding_classification/__init__.py +13 -0
- endoreg_db/views/finding_classification/base.py +0 -0
- endoreg_db/views/finding_classification/finding_classification.py +41 -0
- endoreg_db/views/finding_classification/get_classification_choices.py +54 -0
- endoreg_db/views/media/__init__.py +32 -0
- endoreg_db/views/media/pdf_media.py +411 -0
- endoreg_db/views/media/sensitive_metadata.py +372 -0
- endoreg_db/views/media/video_media.py +275 -0
- endoreg_db/views/meta/__init__.py +7 -0
- endoreg_db/views/meta/sensitive_meta_list.py +102 -0
- endoreg_db/views/meta/sensitive_meta_verification.py +74 -0
- endoreg_db/views/misc/__init__.py +29 -0
- endoreg_db/views/misc/center.py +14 -0
- endoreg_db/views/misc/csrf.py +8 -0
- endoreg_db/views/misc/gender.py +15 -0
- endoreg_db/views/misc/stats.py +255 -0
- endoreg_db/views/misc/upload_views.py +241 -0
- endoreg_db/views/patient/__init__.py +3 -0
- endoreg_db/views/patient/patient.py +253 -0
- endoreg_db/views/patient_examination/__init__.py +11 -0
- endoreg_db/views/patient_examination/patient_examination.py +141 -0
- endoreg_db/views/patient_examination/patient_examination_create.py +58 -0
- endoreg_db/views/patient_examination/patient_examination_detail.py +63 -0
- endoreg_db/views/patient_examination/patient_examination_list.py +72 -0
- endoreg_db/views/patient_examination/video.py +228 -0
- endoreg_db/views/patient_finding/__init__.py +7 -0
- endoreg_db/views/patient_finding/base.py +0 -0
- endoreg_db/views/patient_finding/patient_finding.py +71 -0
- endoreg_db/views/patient_finding/patient_finding_optimized.py +291 -0
- endoreg_db/views/patient_finding_classification/__init__.py +5 -0
- endoreg_db/views/patient_finding_classification/pfc_create.py +75 -0
- endoreg_db/views/report/__init__.py +7 -0
- endoreg_db/views/report/reimport.py +177 -0
- endoreg_db/views/report/report_stream.py +191 -0
- endoreg_db/views/requirement/__init__.py +11 -0
- endoreg_db/views/requirement/evaluate.py +278 -0
- endoreg_db/views/requirement/lookup.py +380 -0
- endoreg_db/views/requirement/lookup_store.py +183 -0
- endoreg_db/views/requirement/requirement_utils.py +87 -0
- endoreg_db/views/requirement_lookup/lookup.py +0 -0
- endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
- endoreg_db/views/stats/__init__.py +13 -0
- endoreg_db/views/stats/stats_views.py +266 -0
- endoreg_db/views/video/__init__.py +49 -0
- endoreg_db/views/video/ai/__init__.py +8 -0
- endoreg_db/views/video/ai/label.py +159 -0
- endoreg_db/views/video/correction.py +529 -0
- endoreg_db/views/video/reimport.py +230 -0
- endoreg_db/views/video/segments_crud.py +709 -0
- endoreg_db/views/video/video_apply_mask.py +49 -0
- endoreg_db/views/video/video_correction.py +22 -0
- endoreg_db/views/video/video_download_processed.py +58 -0
- endoreg_db/views/video/video_examination_viewset.py +242 -0
- endoreg_db/views/video/video_metadata.py +101 -0
- endoreg_db/views/video/video_processing_history.py +25 -0
- endoreg_db/views/video/video_remove_frames.py +49 -0
- endoreg_db/views/video/video_stream.py +334 -0
- endoreg_db-0.8.9.32.dist-info/METADATA +404 -0
- endoreg_db-0.8.9.32.dist-info/RECORD +787 -0
- endoreg_db-0.8.9.32.dist-info/WHEEL +4 -0
- endoreg_db-0.8.9.32.dist-info/licenses/LICENSE +674 -0
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"""
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Video Streaming Views (Phase 3.2)
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Separate view for streaming raw and processed video files.
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Extracted from segmentation.py for better code organization.
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Created: October 9, 2025
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Updated: October 15, 2025 - Added HTTP 206 Range Request Support
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"""
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import os
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import re
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import logging
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import mimetypes
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from pathlib import Path
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from typing import Tuple, Optional
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from django.http import FileResponse, Http404, StreamingHttpResponse
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from rest_framework.views import APIView
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from ...models import VideoFile
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from ...utils.permissions import EnvironmentAwarePermission
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from ...utils.paths import STORAGE_DIR # Import STORAGE_DIR for path resolution
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logger = logging.getLogger(__name__)
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def parse_range_header(range_header: str, file_size: int) -> Tuple[int, int]:
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"""
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Parse HTTP Range header and return (start, end) byte positions.
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Args:
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range_header: HTTP Range header value (e.g., "bytes=0-1023")
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file_size: Total file size in bytes
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Returns:
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Tuple of (start_byte, end_byte) inclusive
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Raises:
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ValueError: If range header is invalid
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"""
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# Expected format: "bytes=start-end" or "bytes=start-"
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match = re.match(r"bytes=(\d+)-(\d*)", range_header)
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if not match:
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raise ValueError(f"Invalid Range header format: {range_header}")
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start = int(match.group(1))
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end_str = match.group(2)
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# If end is not specified, use file size - 1
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end = int(end_str) if end_str else file_size - 1
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# Validate range
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if start >= file_size or start < 0:
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raise ValueError(f"Start byte {start} is out of range (file size: {file_size})")
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if end >= file_size:
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end = file_size - 1
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raise ValueError(f"Invalid range: start ({start}) > end ({end})")
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return start, end
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def stream_file_chunk(file_path: Path, start: int, end: int, chunk_size: int = 8192):
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"""
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Generator that yields chunks of a file within the specified byte range.
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Args:
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file_path: Path to the file
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start: Start byte position (inclusive)
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end: End byte position (inclusive)
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chunk_size: Size of each chunk to yield
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Yields:
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Bytes chunks from the file
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"""
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with open(file_path, "rb") as f:
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f.seek(start)
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remaining = end - start + 1 # +1 because end is inclusive
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while remaining > 0:
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chunk = f.read(min(chunk_size, remaining))
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if not chunk:
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break
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yield chunk
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remaining -= len(chunk)
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def _stream_video_file(
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vf: VideoFile,
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frontend_origin: str,
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file_type: str = "raw",
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range_header: Optional[str] = None,
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) -> FileResponse | StreamingHttpResponse:
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"""
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Helper function to stream a video file with proper headers, CORS support, and HTTP Range Requests.
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Args:
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vf: VideoFile model instance
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frontend_origin: Frontend origin URL for CORS headers
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file_type: Either 'raw' (original video) or 'processed' (anonymized video)
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range_header: HTTP Range header value (e.g., "bytes=0-1023") for partial content requests
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Returns:
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FileResponse: HTTP 200 response streaming the entire file (no range header)
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StreamingHttpResponse: HTTP 206 response streaming partial content (with range header)
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Raises:
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Http404: If video file not found or cannot be accessed
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Note:
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Permissions are handled by the calling view, not in this helper function.
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HTTP 206 Partial Content support is critical for video seeking in browsers.
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"""
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try:
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# Determine which file to stream based on file_type
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if file_type == "raw":
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if (
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hasattr(vf, "active_raw_file")
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and vf.active_raw_file
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and hasattr(vf.active_raw_file, "name")
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):
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file_ref = vf.active_raw_file
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else:
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raise Http404("No raw video file available for this entry")
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elif file_type == "processed":
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if (
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hasattr(vf, "processed_file")
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and vf.processed_file
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and hasattr(vf.processed_file, "name")
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):
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file_ref = vf.processed_file
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else:
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raise Http404("No processed video file available for this entry")
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else:
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raise ValueError(
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f"Invalid file_type: {file_type}. Must be 'raw' or 'processed'."
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)
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# FIX: Handle both relative and absolute paths
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# Django FileField.path returns .name if MEDIA_ROOT is not set
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# Import services store relative paths like "videos/UUID.mp4"
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# We need to resolve to absolute path: STORAGE_DIR / "videos/UUID.mp4"
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file_name = file_ref.name
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if file_name.startswith("/"):
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# Already absolute path
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path = Path(file_name)
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else:
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# Relative path - make absolute by prepending STORAGE_DIR
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path = STORAGE_DIR / str(file_name)
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logger.debug("Resolved relative path '%s' to absolute: %s", file_name, path)
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# Validate file exists on disk
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if not path.exists():
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raise Http404(f"Video file not found on disk: {path}")
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# Validate file size before streaming
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try:
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file_size = path.stat().st_size
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if file_size == 0:
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raise Http404("Video file is empty")
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except OSError as e:
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raise Http404(f"Cannot access video file: {str(e)}")
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# Determine MIME type
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mime, _ = mimetypes.guess_type(str(path))
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content_type = mime or "video/mp4" # Default to mp4 if detection fails
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# ✅ NEW: HTTP Range Request support for video seeking
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if range_header:
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try:
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# Parse Range header
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start, end = parse_range_header(range_header, file_size)
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logger.debug(
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"Range request: bytes=%d-%d (total: %d)", start, end, file_size
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)
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# Stream partial content (HTTP 206)
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response = StreamingHttpResponse(
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stream_file_chunk(path, start, end),
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status=206, # Partial Content
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content_type=content_type,
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)
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# Set Range-specific headers
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response["Content-Range"] = f"bytes {start}-{end}/{file_size}"
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response["Content-Length"] = str(end - start + 1)
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response["Accept-Ranges"] = "bytes"
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response["Content-Disposition"] = f'inline; filename="{path.name}"'
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except ValueError as e:
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# Invalid range header - return 416 Range Not Satisfiable
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logger.warning("Invalid Range header: %s", str(e))
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response = StreamingHttpResponse(
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status=416, # Range Not Satisfiable
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content_type=content_type,
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)
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response["Content-Range"] = f"bytes */{file_size}"
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else:
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# No Range header - stream entire file (HTTP 200)
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try:
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# FileResponse will handle closing; do not close the handle early.
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file_handle = open(path, "rb")
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response = FileResponse(file_handle, content_type=content_type)
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# Set HTTP headers for video streaming
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response["Content-Length"] = str(file_size)
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response["Accept-Ranges"] = (
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"bytes" # Enable HTTP range requests for seeking
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)
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+
response["Content-Disposition"] = f'inline; filename="{path.name}"'
|
|
216
|
+
|
|
217
|
+
except IOError as e:
|
|
218
|
+
raise Http404(f"Cannot open video file: {str(e)}")
|
|
219
|
+
|
|
220
|
+
# CORS headers for frontend access (both HTTP 200 and 206)
|
|
221
|
+
response["Access-Control-Allow-Origin"] = frontend_origin
|
|
222
|
+
response["Access-Control-Allow-Credentials"] = "true"
|
|
223
|
+
response["X-Accel-Buffering"] = "no"
|
|
224
|
+
|
|
225
|
+
return response
|
|
226
|
+
|
|
227
|
+
except Exception as e:
|
|
228
|
+
# Log unexpected errors but don't expose internal details
|
|
229
|
+
logger.error("Unexpected error in _stream_video_file: %s", str(e))
|
|
230
|
+
raise Http404("Video file cannot be streamed")
|
|
231
|
+
|
|
232
|
+
|
|
233
|
+
class VideoStreamView(APIView):
|
|
234
|
+
"""
|
|
235
|
+
Separate view for video streaming to avoid DRF content negotiation issues.
|
|
236
|
+
|
|
237
|
+
Supports streaming both raw (original) and processed (anonymized) videos.
|
|
238
|
+
|
|
239
|
+
Query Parameters:
|
|
240
|
+
type: 'raw' (default) or 'processed' - Selects which video file to stream
|
|
241
|
+
file_type: (deprecated, use 'type') - Legacy parameter for backwards compatibility
|
|
242
|
+
|
|
243
|
+
Examples:
|
|
244
|
+
GET /api/media/videos/1/?type=raw - Stream original raw video
|
|
245
|
+
GET /api/media/videos/1/?type=processed - Stream anonymized/masked video
|
|
246
|
+
GET /api/videostream/1/ - Default to raw video (legacy endpoint)
|
|
247
|
+
|
|
248
|
+
Phase 3.2 Implementation:
|
|
249
|
+
- Supports dual video comparison (raw vs processed)
|
|
250
|
+
- Backward compatible with legacy ?file_type= parameter
|
|
251
|
+
- Proper error handling with Http404
|
|
252
|
+
- CORS support for frontend access
|
|
253
|
+
- HTTP range support for video seeking
|
|
254
|
+
"""
|
|
255
|
+
|
|
256
|
+
permission_classes = [EnvironmentAwarePermission]
|
|
257
|
+
|
|
258
|
+
def get(self, request, pk=None):
|
|
259
|
+
"""
|
|
260
|
+
Stream raw or anonymized video file with HTTP Range Request and CORS support.
|
|
261
|
+
|
|
262
|
+
Supports HTTP 206 Partial Content for video seeking functionality.
|
|
263
|
+
|
|
264
|
+
Args:
|
|
265
|
+
request: HTTP request object
|
|
266
|
+
pk: Video ID (primary key)
|
|
267
|
+
|
|
268
|
+
Returns:
|
|
269
|
+
FileResponse: HTTP 200 streaming entire video file (no range header)
|
|
270
|
+
StreamingHttpResponse: HTTP 206 streaming partial content (with range header)
|
|
271
|
+
|
|
272
|
+
Raises:
|
|
273
|
+
Http404: If video not found or file cannot be accessed
|
|
274
|
+
"""
|
|
275
|
+
if pk is None:
|
|
276
|
+
raise Http404("Video ID is required")
|
|
277
|
+
|
|
278
|
+
# Initialize variables in outer scope
|
|
279
|
+
video_id_int = None
|
|
280
|
+
|
|
281
|
+
try:
|
|
282
|
+
# Validate video_id is numeric
|
|
283
|
+
try:
|
|
284
|
+
video_id_int = int(pk)
|
|
285
|
+
except (ValueError, TypeError):
|
|
286
|
+
raise Http404("Invalid video ID format")
|
|
287
|
+
|
|
288
|
+
# Support both 'type' (frontend standard) and 'file_type' (legacy)
|
|
289
|
+
# Priority: type > file_type > default 'raw'
|
|
290
|
+
file_type = "raw" # Default value
|
|
291
|
+
try:
|
|
292
|
+
file_type_param = request.query_params.get(
|
|
293
|
+
"type"
|
|
294
|
+
) or request.query_params.get("file_type")
|
|
295
|
+
if file_type_param:
|
|
296
|
+
file_type = file_type_param.lower()
|
|
297
|
+
|
|
298
|
+
if file_type not in ["raw", "processed"]:
|
|
299
|
+
logger.warning(
|
|
300
|
+
"Invalid file_type '%s', defaulting to 'raw'", file_type
|
|
301
|
+
)
|
|
302
|
+
file_type = "raw"
|
|
303
|
+
|
|
304
|
+
except Exception as e:
|
|
305
|
+
logger.warning(
|
|
306
|
+
"Error parsing file_type parameter: %s, defaulting to 'raw'", e
|
|
307
|
+
)
|
|
308
|
+
file_type = "raw"
|
|
309
|
+
|
|
310
|
+
# Fetch video from database
|
|
311
|
+
vf = VideoFile.objects.get(pk=video_id_int)
|
|
312
|
+
|
|
313
|
+
# Get frontend origin for CORS
|
|
314
|
+
frontend_origin = os.environ.get("FRONTEND_ORIGIN", "http://localhost:8000")
|
|
315
|
+
|
|
316
|
+
# ✅ NEW: Extract Range header for HTTP 206 support
|
|
317
|
+
range_header = request.META.get("HTTP_RANGE")
|
|
318
|
+
|
|
319
|
+
# Stream the video file with optional range support
|
|
320
|
+
return _stream_video_file(vf, frontend_origin, file_type, range_header)
|
|
321
|
+
|
|
322
|
+
except VideoFile.DoesNotExist:
|
|
323
|
+
raise Http404(f"Video with ID {pk} not found")
|
|
324
|
+
|
|
325
|
+
except Http404:
|
|
326
|
+
# Re-raise Http404 exceptions as they should bubble up
|
|
327
|
+
raise
|
|
328
|
+
|
|
329
|
+
except Exception as e:
|
|
330
|
+
# Log unexpected errors and convert to Http404
|
|
331
|
+
logger.error(
|
|
332
|
+
"Unexpected error in VideoStreamView for video_id=%s: %s", pk, str(e)
|
|
333
|
+
)
|
|
334
|
+
raise Http404("Video streaming failed")
|