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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import logging
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# Removed hash utils, datetime, random, os, timezone, sha256 imports
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# Removed icecream import (was used in old save logic)
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from typing import TYPE_CHECKING, Any, Dict, Type, cast
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from django.db import models
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# Import models needed for type hints and FKs
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from ..state import SensitiveMetaState # Needed for post-save state check
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# Import logic functions
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from . import sensitive_meta_logic as logic
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if TYPE_CHECKING:
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from ..administration import (
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Center,
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Examiner,
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Patient, # Keep for type hinting if needed
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)
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from ..medical import PatientExamination
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from ..other import Gender
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# from ..state import SensitiveMetaState # Already imported above
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logger = logging.getLogger(__name__) # Add logger instance
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# SECRET_SALT moved to logic
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class SensitiveMeta(models.Model):
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"""
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Stores potentially sensitive information extracted from media.
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Logic for creation, hashing, pseudo-anonymization, and saving is in sensitive_meta_logic.py.
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"""
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# --- Examination and Patient Info ---
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examination_date = models.DateField(blank=True, null=True)
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examination_time = models.TimeField(blank=True, null=True)
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casenumber = models.CharField(max_length=255, blank=True, null=True)
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file_path = models.CharField(max_length=1024, blank=True, null=True)
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# --- Core FKs ---
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pseudo_patient = models.ForeignKey(
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"Patient",
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on_delete=models.CASCADE,
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blank=True,
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null=True,
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help_text="FK to the pseudo-anonymized Patient record.",
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)
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pseudo_examination = models.ForeignKey(
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"PatientExamination",
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on_delete=models.CASCADE,
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blank=True,
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null=True,
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help_text="FK to the pseudo-anonymized PatientExamination record.",
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)
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patient_gender = models.ForeignKey(
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"Gender", on_delete=models.CASCADE, blank=True, null=True
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)
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examiners = models.ManyToManyField(
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"Examiner", blank=True, help_text="Pseudo-anonymized examiner(s)"
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)
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center = models.ForeignKey(
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"Center", on_delete=models.CASCADE, blank=True, null=True
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)
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# --- Names and DOB ---
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patient_first_name = models.CharField(max_length=255, blank=True, null=True)
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patient_last_name = models.CharField(max_length=255, blank=True, null=True)
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patient_dob = models.DateTimeField(
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blank=True, null=True, help_text="Date of birth (can be auto-generated)."
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)
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examiner_first_name = models.CharField(
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max_length=255, blank=True, null=True, editable=False
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)
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examiner_last_name = models.CharField(
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max_length=255, blank=True, null=True, editable=False
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)
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# --- Hashes ---
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patient_hash = models.CharField(
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max_length=64, blank=True, null=True, editable=False, db_index=True
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)
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examination_hash = models.CharField(
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max_length=64, blank=True, null=True, editable=False, db_index=True
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)
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# --- Endoscope Info ---
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endoscope_type = models.CharField(max_length=255, blank=True, null=True)
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endoscope_sn = models.CharField(max_length=255, blank=True, null=True)
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# --- External patient ID ---
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external_id = models.ForeignKey(
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"PatientExternalID", on_delete=models.CASCADE, blank=True, null=True
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)
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if TYPE_CHECKING:
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pseudo_patient: models.ForeignKey["Patient|None"]
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patient_gender: models.ForeignKey["Gender|None"]
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pseudo_examination: models.ForeignKey["PatientExamination|None"]
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state: models.ForeignKey[
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"SensitiveMetaState|None"
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] # Assuming related_name='state' is defined on SensitiveMetaState.origin
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center: models.ForeignKey["Center|None"]
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@property
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def external_id_origin(self) -> str | None:
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"""Returns the origin system from the linked external ID, if available."""
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if self.external_id:
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return self.external_id.origin
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return None
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# --- Text Fields ---
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text = models.TextField(blank=True, null=True)
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anonymized_text = models.TextField(blank=True, null=True)
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# --- Anonymization helper method ---
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create_anonymized_record = logic._create_anonymized_record
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# --- State ---
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@property
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def state_verified(self) -> bool | None:
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"""
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Convenience alias to check if the related state is verified.
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Returns None if state is not set.
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"""
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if hasattr(self, "state") and self.state is not None:
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return self.state.is_verified
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return None
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@staticmethod
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def _generate_random_dob():
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# Delegate to logic
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return logic.generate_random_dob()
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@staticmethod
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def _generate_random_examination_date():
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# Delegate to logic
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return logic.generate_random_examination_date()
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@classmethod
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def create_from_dict(cls: Type["SensitiveMeta"], data: Dict[str, Any]):
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"""Creates a SensitiveMeta instance from a dictionary using external logic."""
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# Delegate to logic function
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return logic.create_sensitive_meta_from_dict(cls, data)
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# --- Methods related to pseudo-entities are now primarily handled within save logic ---
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def get_pseudo_examiner(self) -> "Examiner | None":
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"""Returns the linked pseudo examiner, if one exists."""
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if self.pk:
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return self.examiners.first()
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return None # Cannot determine before saving and linking
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# --- Update method delegates to logic ---
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def update_from_dict(self, data: Dict[str, Any]):
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"""Updates the instance from a dictionary using external logic."""
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# Delegate to logic function
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return logic.update_sensitive_meta_from_dict(self, data)
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# --- String representation ---
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def __str__(self):
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# Keep this method for basic representation, ensure fields are accessed safely
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center_name = self.center.name if self.center else "None"
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gender_str = str(self.patient_gender) if self.patient_gender else "None"
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dob_str = (
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str(self.patient_dob.date()) if self.patient_dob else "None"
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) # Show only date part
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exam_date_str = str(self.examination_date) if self.examination_date else "None"
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examiners_str = "[Not saved yet]"
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if self.pk:
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try:
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# Use prefetch_related in queries accessing this for efficiency
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examiners_str = (
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", ".join([str(e) for e in self.examiners.all()]) or "[None]"
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)
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except Exception as e:
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examiners_str = f"[Error: {e}]"
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state_verified = "Unknown"
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if self.pk:
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# Access state verification through the related state object
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state_verified = str(self.is_verified)
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else:
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state_verified = "[Not saved yet]"
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return (
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f"SensitiveMeta(pk={self.pk}): "
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f"Patient={self.patient_last_name}, {self.patient_first_name} (*{dob_str}, {gender_str}), "
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f"ExamDate={exam_date_str}, Center={center_name}, "
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f"Examiners={examiners_str}, StateVerified={state_verified}, "
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f"PatientHash={str(self.patient_hash)[-8:] if self.patient_hash else 'None'}, " # Show last 8 chars
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f"ExamHash={str(self.examination_hash)[-8:] if self.examination_hash else 'None'}" # Show last 8 chars
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)
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@property
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def state_safe(self) -> "SensitiveMetaState":
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state = self.state
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if not state:
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raise SensitiveMetaState.DoesNotExist(
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"SensitiveMetaState does not exist for this SensitiveMeta instance."
|
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207
|
+
)
|
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208
|
+
return state
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209
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+
|
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210
|
+
@property
|
|
211
|
+
def is_verified(self):
|
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212
|
+
"""
|
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213
|
+
Checks if the instance is verified based on the related state object.
|
|
214
|
+
"""
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215
|
+
# Use try-except for robustness, especially if state might not exist yet
|
|
216
|
+
try:
|
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217
|
+
# Access the related state object directly via the 'state' attribute
|
|
218
|
+
# This assumes the related_name on SensitiveMetaState.origin is 'state'
|
|
219
|
+
return self.state_safe.is_verified
|
|
220
|
+
except SensitiveMetaState.DoesNotExist:
|
|
221
|
+
# If the state object doesn't exist, it's not verified
|
|
222
|
+
return False
|
|
223
|
+
except AttributeError:
|
|
224
|
+
# If the 'state' attribute doesn't exist (e.g., before first save), it's not verified
|
|
225
|
+
return False
|
|
226
|
+
|
|
227
|
+
def get_or_create_state(self) -> "SensitiveMetaState":
|
|
228
|
+
"""
|
|
229
|
+
Gets the related SensitiveMetaState instance, creating one if it doesn't exist.
|
|
230
|
+
Does not save the SensitiveMeta instance itself.
|
|
231
|
+
"""
|
|
232
|
+
try:
|
|
233
|
+
state = self.state_safe
|
|
234
|
+
return state
|
|
235
|
+
|
|
236
|
+
except SensitiveMetaState.DoesNotExist:
|
|
237
|
+
# If it doesn't exist, create it
|
|
238
|
+
logger.info("Creating new SensitiveMetaState for SensitiveMeta %s", self.pk)
|
|
239
|
+
# Create the state, linking it back to this instance
|
|
240
|
+
# The 'origin' field on SensitiveMetaState points back to this SensitiveMeta instance
|
|
241
|
+
new_state = SensitiveMetaState.objects.create(origin=self)
|
|
242
|
+
# Assign the newly created state to the instance's 'state' attribute
|
|
243
|
+
# This avoids needing to query again immediately
|
|
244
|
+
self.state = new_state
|
|
245
|
+
return new_state
|
|
246
|
+
except AttributeError:
|
|
247
|
+
# Fallback if related_name is not 'state' or instance not saved yet (no PK)
|
|
248
|
+
if self.pk:
|
|
249
|
+
state, created = SensitiveMetaState.objects.get_or_create(origin=self)
|
|
250
|
+
if created:
|
|
251
|
+
logger.info(
|
|
252
|
+
"Created new SensitiveMetaState for SensitiveMeta %s (via get_or_create)",
|
|
253
|
+
self.pk,
|
|
254
|
+
)
|
|
255
|
+
# Link the state back to the instance in memory
|
|
256
|
+
self.state = state
|
|
257
|
+
return state
|
|
258
|
+
else:
|
|
259
|
+
# Cannot create state if the main instance has no PK
|
|
260
|
+
raise ValueError(
|
|
261
|
+
"Cannot get or create state for an unsaved SensitiveMeta instance."
|
|
262
|
+
)
|
|
263
|
+
|
|
264
|
+
def __repr__(self):
|
|
265
|
+
return self.__str__()
|
|
266
|
+
|
|
267
|
+
# --- Hashing methods delegate to logic ---
|
|
268
|
+
def get_patient_hash(self, salt=None):
|
|
269
|
+
"""Calculates the patient hash using external logic."""
|
|
270
|
+
# Use default salt from logic if None is passed
|
|
271
|
+
salt_to_use = salt if salt is not None else logic.SECRET_SALT
|
|
272
|
+
# Delegate to logic function
|
|
273
|
+
return logic.calculate_patient_hash(self, salt=salt_to_use)
|
|
274
|
+
|
|
275
|
+
def get_patient_examination_hash(self, salt=None):
|
|
276
|
+
"""Calculates the examination hash using external logic."""
|
|
277
|
+
salt_to_use = salt if salt is not None else logic.SECRET_SALT
|
|
278
|
+
# Delegate to logic function
|
|
279
|
+
return logic.calculate_examination_hash(self, salt=salt_to_use)
|
|
280
|
+
|
|
281
|
+
# --- Save method orchestrates calls to logic ---
|
|
282
|
+
def save(self, *args, **kwargs):
|
|
283
|
+
"""
|
|
284
|
+
Saves the SensitiveMeta instance, ensuring data integrity, hash calculation, pseudo-entity linking, and related state management using external logic.
|
|
285
|
+
|
|
286
|
+
This method performs pre-save operations via external logic, persists the instance, ensures the related SensitiveMetaState exists, and links the appropriate examiner to the instance.
|
|
287
|
+
"""
|
|
288
|
+
# 1. Call the main logic function to perform pre-save checks, data generation,
|
|
289
|
+
# and creation/linking of pseudo patient/examination FKs.
|
|
290
|
+
# This function modifies the instance fields (hashes, FKs, dates).
|
|
291
|
+
# It returns the examiner instance to be linked *after* saving.
|
|
292
|
+
examiner_to_link = logic.perform_save_logic(self) # Pass only self
|
|
293
|
+
|
|
294
|
+
# 2. Call the original Django save method to save the instance itself
|
|
295
|
+
# (including updated FKs, hashes, dates).
|
|
296
|
+
super().save(*args, **kwargs) # Pass original args/kwargs
|
|
297
|
+
|
|
298
|
+
# 3. Ensure SensitiveMetaState exists *after* saving the main instance
|
|
299
|
+
# Use related name 'state' if defined, otherwise access via manager.
|
|
300
|
+
if self.pk: # Ensure we have a PK
|
|
301
|
+
try:
|
|
302
|
+
# Check if the related state object already exists using the related manager
|
|
303
|
+
_ = self.state
|
|
304
|
+
except SensitiveMetaState.DoesNotExist:
|
|
305
|
+
# If not, create a new one, linking it to the saved instance
|
|
306
|
+
SensitiveMetaState.objects.create(origin=self)
|
|
307
|
+
except AttributeError:
|
|
308
|
+
# Fallback check if 'state' related_name is missing
|
|
309
|
+
if not SensitiveMetaState.objects.filter(origin=self).exists():
|
|
310
|
+
SensitiveMetaState.objects.create(origin=self)
|
|
311
|
+
|
|
312
|
+
# 4. Handle ManyToMany linking (examiners) *after* the instance has a PK.
|
|
313
|
+
if (
|
|
314
|
+
examiner_to_link
|
|
315
|
+
and self.pk
|
|
316
|
+
and not self.examiners.filter(pk=examiner_to_link.pk).exists()
|
|
317
|
+
):
|
|
318
|
+
self.examiners.add(examiner_to_link)
|
|
319
|
+
# Adding to M2M handles its own DB interaction, no second super().save() needed.
|
|
320
|
+
|
|
321
|
+
def mark_dob_verified(self):
|
|
322
|
+
"""
|
|
323
|
+
Mark the associated date of birth as verified in the related SensitiveMetaState.
|
|
324
|
+
"""
|
|
325
|
+
state = self.get_or_create_state()
|
|
326
|
+
state.mark_dob_verified()
|
|
327
|
+
|
|
328
|
+
def mark_names_verified(self):
|
|
329
|
+
"""
|
|
330
|
+
Mark the patient's names as verified in the associated verification state.
|
|
331
|
+
|
|
332
|
+
This method ensures the related SensitiveMetaState exists and updates its status to indicate that the patient's names have been verified.
|
|
333
|
+
"""
|
|
334
|
+
state = self.get_or_create_state()
|
|
335
|
+
state.mark_names_verified()
|
|
336
|
+
|
|
337
|
+
@classmethod
|
|
338
|
+
def _update_name_db(cls, first_name, last_name):
|
|
339
|
+
# Delegate to logic
|
|
340
|
+
"""
|
|
341
|
+
Update the name database with the provided first and last names using external logic.
|
|
342
|
+
|
|
343
|
+
This method delegates the update operation to the external logic module responsible for managing name data.
|
|
344
|
+
"""
|
|
345
|
+
logic.update_name_db(first_name, last_name)
|