endoreg-db 0.8.5.1__py3-none-any.whl
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- endoreg_db/__init__.py +0 -0
- endoreg_db/admin.py +92 -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 +18 -0
- endoreg_db/assets/dummy_model.ckpt +1 -0
- endoreg_db/codemods/readme.md +88 -0
- endoreg_db/codemods/rename_datetime_fields.py +92 -0
- endoreg_db/config/__init__.py +0 -0
- endoreg_db/config/env.py +101 -0
- endoreg_db/data/__init__.py +144 -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 +91 -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/examination/examinations/data.yaml +72 -0
- endoreg_db/data/examination/time/data.yaml +48 -0
- endoreg_db/data/examination/time-type/data.yaml +8 -0
- endoreg_db/data/examination/type/data.yaml +17 -0
- endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
- endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
- endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
- endoreg_db/data/finding/anatomy_colon.yaml +128 -0
- endoreg_db/data/finding/colonoscopy.yaml +40 -0
- endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
- endoreg_db/data/finding/complication.yaml +16 -0
- endoreg_db/data/finding/data.yaml +105 -0
- endoreg_db/data/finding/examination_setting.yaml +16 -0
- endoreg_db/data/finding/medication_related.yaml +18 -0
- endoreg_db/data/finding/outcome.yaml +12 -0
- endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
- endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
- endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
- endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
- endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
- endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
- endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
- endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
- endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
- endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
- endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
- endoreg_db/data/finding_classification/medication_related.yaml +23 -0
- endoreg_db/data/finding_classification/visualized.yaml +33 -0
- endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
- endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
- endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
- endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
- endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
- endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
- endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
- endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
- endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
- endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
- endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
- endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
- endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
- endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
- endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
- endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
- endoreg_db/data/finding_type/data.yaml +43 -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/age.yaml +26 -0
- endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
- endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
- endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
- endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
- endoreg_db/data/requirement/disease_misc.yaml +12 -0
- endoreg_db/data/requirement/disease_renal.yaml +96 -0
- endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
- endoreg_db/data/requirement/event_cardiology.yaml +251 -0
- endoreg_db/data/requirement/event_requirements.yaml +145 -0
- endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
- endoreg_db/data/requirement/gender.yaml +25 -0
- endoreg_db/data/requirement/lab_value.yaml +441 -0
- endoreg_db/data/requirement/medication.yaml +93 -0
- endoreg_db/data/requirement_operator/age.yaml +13 -0
- endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
- endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
- endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
- endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
- endoreg_db/data/requirement_set_type/data.yaml +20 -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 +11 -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 +19 -0
- endoreg_db/factories/__init__.py +0 -0
- endoreg_db/forms/__init__.py +5 -0
- endoreg_db/forms/examination_form.py +11 -0
- endoreg_db/forms/patient_finding_intervention_form.py +18 -0
- endoreg_db/forms/patient_form.py +27 -0
- endoreg_db/forms/questionnaires/__init__.py +1 -0
- endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
- endoreg_db/forms/settings/__init__.py +8 -0
- endoreg_db/forms/unit.py +6 -0
- endoreg_db/helpers/__init__.py +0 -0
- endoreg_db/helpers/count_db.py +45 -0
- endoreg_db/helpers/data_loader.py +208 -0
- endoreg_db/helpers/default_objects.py +378 -0
- endoreg_db/helpers/download_segmentation_model.py +31 -0
- endoreg_db/helpers/interact.py +6 -0
- endoreg_db/helpers/test_video_helper.py +119 -0
- endoreg_db/logger_conf.py +140 -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 +125 -0
- endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
- endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
- endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
- endoreg_db/management/commands/fix_video_paths.py +165 -0
- endoreg_db/management/commands/import_fallback_video.py +203 -0
- endoreg_db/management/commands/import_report.py +298 -0
- endoreg_db/management/commands/import_video.py +423 -0
- endoreg_db/management/commands/import_video_with_classification.py +367 -0
- endoreg_db/management/commands/init_default_ai_model.py +112 -0
- endoreg_db/management/commands/load_ai_model_data.py +77 -0
- endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
- endoreg_db/management/commands/load_base_db_data.py +192 -0
- endoreg_db/management/commands/load_center_data.py +68 -0
- endoreg_db/management/commands/load_contraindication_data.py +41 -0
- endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
- endoreg_db/management/commands/load_disease_classification_data.py +41 -0
- endoreg_db/management/commands/load_disease_data.py +62 -0
- endoreg_db/management/commands/load_distribution_data.py +66 -0
- endoreg_db/management/commands/load_endoscope_data.py +68 -0
- endoreg_db/management/commands/load_event_data.py +41 -0
- endoreg_db/management/commands/load_examination_data.py +75 -0
- endoreg_db/management/commands/load_examination_indication_data.py +86 -0
- endoreg_db/management/commands/load_finding_data.py +128 -0
- endoreg_db/management/commands/load_gender_data.py +44 -0
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
- endoreg_db/management/commands/load_information_source.py +51 -0
- endoreg_db/management/commands/load_lab_value_data.py +50 -0
- endoreg_db/management/commands/load_medication_data.py +103 -0
- endoreg_db/management/commands/load_name_data.py +37 -0
- endoreg_db/management/commands/load_organ_data.py +43 -0
- endoreg_db/management/commands/load_pdf_type_data.py +61 -0
- endoreg_db/management/commands/load_profession_data.py +44 -0
- endoreg_db/management/commands/load_qualification_data.py +59 -0
- endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
- endoreg_db/management/commands/load_requirement_data.py +180 -0
- endoreg_db/management/commands/load_risk_data.py +56 -0
- endoreg_db/management/commands/load_shift_data.py +60 -0
- endoreg_db/management/commands/load_tag_data.py +57 -0
- endoreg_db/management/commands/load_unit_data.py +46 -0
- endoreg_db/management/commands/load_user_groups.py +28 -0
- endoreg_db/management/commands/register_ai_model.py +64 -0
- endoreg_db/management/commands/reset_celery_schedule.py +9 -0
- endoreg_db/management/commands/setup_endoreg_db.py +381 -0
- endoreg_db/management/commands/start_filewatcher.py +106 -0
- endoreg_db/management/commands/storage_management.py +548 -0
- endoreg_db/management/commands/summarize_db_content.py +189 -0
- endoreg_db/management/commands/validate_video.py +204 -0
- endoreg_db/management/commands/validate_video_files.py +161 -0
- endoreg_db/management/commands/video_validation.py +22 -0
- endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
- endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
- endoreg_db/mermaid/binary_classification_annotation.md +50 -0
- endoreg_db/mermaid/classification.md +8 -0
- endoreg_db/mermaid/examination.md +8 -0
- endoreg_db/mermaid/findings.md +7 -0
- endoreg_db/mermaid/image_classification.md +28 -0
- endoreg_db/mermaid/interventions.md +8 -0
- endoreg_db/mermaid/morphology.md +8 -0
- endoreg_db/mermaid/patient_creation.md +14 -0
- endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
- endoreg_db/migrations/0001_initial.py +1857 -0
- endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
- endoreg_db/migrations/0003_add_center_display_name.py +30 -0
- endoreg_db/migrations/__init__.py +0 -0
- endoreg_db/models/__init__.py +359 -0
- endoreg_db/models/administration/__init__.py +116 -0
- endoreg_db/models/administration/ai/__init__.py +9 -0
- endoreg_db/models/administration/ai/active_model.py +35 -0
- endoreg_db/models/administration/ai/ai_model.py +156 -0
- endoreg_db/models/administration/ai/model_type.py +41 -0
- endoreg_db/models/administration/case/__init__.py +19 -0
- endoreg_db/models/administration/case/case.py +114 -0
- endoreg_db/models/administration/case/case_template/__init__.py +15 -0
- endoreg_db/models/administration/case/case_template/case_template.py +125 -0
- endoreg_db/models/administration/case/case_template/case_template_rule.py +269 -0
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- endoreg_db/utils/pydantic_models/__init__.py +6 -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/lab_value_operators.py +578 -0
- endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
- endoreg_db/utils/setup_config.py +177 -0
- endoreg_db/utils/translation.py +27 -0
- endoreg_db/utils/uuid.py +4 -0
- endoreg_db/utils/validate_endo_roi.py +19 -0
- endoreg_db/utils/validate_subcategory_dict.py +91 -0
- endoreg_db/utils/validate_video_detailed.py +357 -0
- endoreg_db/utils/video/__init__.py +26 -0
- endoreg_db/utils/video/extract_frames.py +88 -0
- endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
- endoreg_db/utils/video/names.py +42 -0
- endoreg_db/utils/video/streaming_processor.py +312 -0
- endoreg_db/utils/video/video_splitter.py +94 -0
- endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
- endoreg_db/views/__init__.py +272 -0
- endoreg_db/views/anonymization/__init__.py +27 -0
- endoreg_db/views/anonymization/media_management.py +454 -0
- endoreg_db/views/anonymization/overview.py +216 -0
- endoreg_db/views/anonymization/validate.py +107 -0
- endoreg_db/views/auth/__init__.py +13 -0
- endoreg_db/views/auth/keycloak.py +113 -0
- endoreg_db/views/examination/__init__.py +33 -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 +59 -0
- endoreg_db/views/examination/get_finding_classifications.py +36 -0
- endoreg_db/views/examination/get_findings.py +41 -0
- endoreg_db/views/examination/get_instruments.py +18 -0
- endoreg_db/views/examination/get_interventions.py +14 -0
- endoreg_db/views/finding/__init__.py +9 -0
- endoreg_db/views/finding/finding.py +112 -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 +42 -0
- endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
- endoreg_db/views/label/__init__.py +5 -0
- endoreg_db/views/label/label.py +15 -0
- endoreg_db/views/label_video_segment/__init__.py +16 -0
- endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
- endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
- endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
- endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
- endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
- endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
- endoreg_db/views/label_video_segment/validate.py +226 -0
- endoreg_db/views/media/__init__.py +45 -0
- endoreg_db/views/media/pdf_media.py +386 -0
- endoreg_db/views/media/segments.py +71 -0
- endoreg_db/views/media/sensitive_metadata.py +314 -0
- endoreg_db/views/media/video_media.py +272 -0
- endoreg_db/views/media/video_segments.py +524 -0
- endoreg_db/views/meta/__init__.py +15 -0
- endoreg_db/views/meta/available_files_list.py +146 -0
- endoreg_db/views/meta/report_meta.py +53 -0
- endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
- endoreg_db/views/meta/sensitive_meta_list.py +104 -0
- endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
- endoreg_db/views/misc/__init__.py +63 -0
- endoreg_db/views/misc/center.py +13 -0
- endoreg_db/views/misc/csrf.py +7 -0
- endoreg_db/views/misc/gender.py +14 -0
- endoreg_db/views/misc/secure_file_serving_view.py +80 -0
- endoreg_db/views/misc/secure_file_url_view.py +84 -0
- endoreg_db/views/misc/secure_url_validate.py +79 -0
- endoreg_db/views/misc/stats.py +220 -0
- endoreg_db/views/misc/translation.py +182 -0
- endoreg_db/views/misc/upload_views.py +240 -0
- endoreg_db/views/patient/__init__.py +5 -0
- endoreg_db/views/patient/patient.py +210 -0
- endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
- endoreg_db/views/patient_examination/__init__.py +11 -0
- endoreg_db/views/patient_examination/patient_examination.py +140 -0
- endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
- endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
- endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
- endoreg_db/views/patient_examination/video.py +194 -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 +64 -0
- endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
- endoreg_db/views/patient_finding_classification/__init__.py +5 -0
- endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
- endoreg_db/views/patient_finding_location/__init__.py +5 -0
- endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
- endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
- endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
- endoreg_db/views/pdf/__init__.py +11 -0
- endoreg_db/views/pdf/pdf_media.py +239 -0
- endoreg_db/views/pdf/pdf_stream_views.py +127 -0
- endoreg_db/views/pdf/reimport.py +161 -0
- endoreg_db/views/report/__init__.py +9 -0
- endoreg_db/views/report/report_list.py +112 -0
- endoreg_db/views/report/report_with_secure_url.py +28 -0
- endoreg_db/views/report/start_examination.py +7 -0
- endoreg_db/views/requirement/__init__.py +10 -0
- endoreg_db/views/requirement/evaluate.py +279 -0
- endoreg_db/views/requirement/lookup.py +483 -0
- endoreg_db/views/requirement/lookup_store.py +252 -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 +229 -0
- endoreg_db/views/video/__init__.py +61 -0
- endoreg_db/views/video/correction.py +530 -0
- endoreg_db/views/video/reimport.py +195 -0
- endoreg_db/views/video/segmentation.py +274 -0
- endoreg_db/views/video/task_status.py +49 -0
- endoreg_db/views/video/timeline.py +46 -0
- endoreg_db/views/video/video_analyze.py +52 -0
- endoreg_db/views/video/video_apply_mask.py +48 -0
- endoreg_db/views/video/video_correction.py +21 -0
- endoreg_db/views/video/video_download_processed.py +58 -0
- endoreg_db/views/video/video_examination_viewset.py +329 -0
- endoreg_db/views/video/video_media.py +158 -0
- endoreg_db/views/video/video_meta.py +29 -0
- endoreg_db/views/video/video_processing_history.py +24 -0
- endoreg_db/views/video/video_remove_frames.py +48 -0
- endoreg_db/views/video/video_stream.py +306 -0
- endoreg_db/views.py +0 -0
- endoreg_db-0.8.5.1.dist-info/METADATA +383 -0
- endoreg_db-0.8.5.1.dist-info/RECORD +794 -0
- endoreg_db-0.8.5.1.dist-info/WHEEL +4 -0
- endoreg_db-0.8.5.1.dist-info/licenses/LICENSE +674 -0
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import logging
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import os
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import random
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import re # Neu hinzugefügt für Regex-Pattern
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from datetime import date, datetime, timedelta
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from hashlib import sha256
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from typing import TYPE_CHECKING, Any, Dict, Optional, Type
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from django.db import transaction
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from django.utils import timezone
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from endoreg_db.utils import guess_name_gender
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# Assuming these utils are correctly located
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from endoreg_db.utils.hashs import get_patient_examination_hash, get_patient_hash
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# Import models needed for logic, use local imports inside functions if needed to break cycles
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from ..administration import Center, Examiner, FirstName, LastName, Patient
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from ..medical import PatientExamination
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from ..other import Gender
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from ..state import SensitiveMetaState
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if TYPE_CHECKING:
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from .sensitive_meta import SensitiveMeta # Import model for type hinting
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logger = logging.getLogger(__name__)
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SECRET_SALT = os.getenv("DJANGO_SALT", "default_salt")
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DEFAULT_UNKNOWN_NAME = "unknown"
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# Regex-Pattern für verschiedene Datumsformate
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ISO_RX = re.compile(r"^\d{4}-\d{2}-\d{2}$")
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DE_RX = re.compile(r"^\d{2}\.\d{2}\.\d{4}$")
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def parse_any_date(s: str) -> Optional[date]:
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"""
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Parst Datumsstring mit Priorität auf deutsches Format (DD.MM.YYYY).
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Unterstützte Formate:
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1. DD.MM.YYYY (Priorität) - deutsches Format
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2. YYYY-MM-DD (Fallback) - ISO-Format
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3. Erweiterte Fallbacks über dateparser
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Args:
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s: Datumsstring zum Parsen
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Returns:
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date-Objekt oder None bei ungültigem/fehlendem Input
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"""
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return None
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s = s.strip()
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# 1. German dd.mm.yyyy (PRIORITÄT)
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if DE_RX.match(s):
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try:
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except ValueError as e:
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logger.warning(f"Invalid German date format '{s}': {e}")
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return None
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# 2. ISO yyyy-mm-dd (Fallback für Rückwärtskompatibilität)
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try:
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return date.fromisoformat(s)
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logger.warning(f"Invalid ISO date format '{s}': {e}")
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return None
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# 3. Extended fallbacks
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try:
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# Try standard datetime parsing
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return datetime.fromisoformat(s).date()
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except Exception:
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pass
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try:
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# Try dateparser with German locale preference
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import dateparser
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dt = dateparser.parse(s, settings={"DATE_ORDER": "DMY", "PREFER_DAY_OF_MONTH": "first"})
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return dt.date() if dt else None
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except Exception as e:
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logger.debug(f"Dateparser fallback failed for '{s}': {e}")
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return None
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def format_date_german(d: Optional[date]) -> str:
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"""
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Formatiert date-Objekt als deutsches Datumsformat (DD.MM.YYYY).
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Args:
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Returns:
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Formatiertes Datum als String oder leerer String bei None
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"""
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return ""
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return d.strftime("%d.%m.%Y")
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def format_date_iso(d: Optional[date]) -> str:
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"""
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Formatiert date-Objekt als ISO-Format (YYYY-MM-DD).
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Args:
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Returns:
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Formatiertes Datum als String oder leerer String bei None
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"""
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return ""
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return d.isoformat()
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def generate_random_dob() -> datetime:
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"""Generates a random timezone-aware datetime between 1920-01-01 and 2000-12-31."""
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start_date = date(1920, 1, 1)
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end_date = date(2000, 12, 31)
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time_between_dates = end_date - start_date
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days_between_dates = time_between_dates.days
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random_number_of_days = random.randrange(days_between_dates)
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random_date = start_date + timedelta(days=random_number_of_days)
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random_datetime = datetime.combine(random_date, datetime.min.time())
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return timezone.make_aware(random_datetime)
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def generate_random_examination_date() -> date:
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"""Generates a random date within the last 20 years."""
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today = date.today()
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start_date = today - timedelta(days=20 * 365) # Approximate 20 years back
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time_between_dates = today - start_date
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days_between_dates = time_between_dates.days
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random_number_of_days = random.randrange(days_between_dates)
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random_date = start_date + timedelta(days=random_number_of_days)
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return random_date
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def update_name_db(first_name: Optional[str], last_name: Optional[str]):
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"""Adds first and last names to the respective lookup tables if they don't exist."""
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if first_name:
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FirstName.objects.get_or_create(name=first_name)
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if last_name:
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LastName.objects.get_or_create(name=last_name)
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def calculate_patient_hash(instance: "SensitiveMeta", salt: str = SECRET_SALT) -> str:
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"""Calculates the patient hash for the instance."""
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dob = instance.patient_dob
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first_name = instance.patient_first_name
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last_name = instance.patient_last_name
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center = instance.center
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if not dob:
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raise ValueError("Patient DOB is required to calculate patient hash.")
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if not center:
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raise ValueError("Center is required to calculate patient hash.")
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assert first_name is not None, "First name is required to calculate patient hash."
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assert last_name is not None, "Last name is required to calculate patient hash."
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hash_str = get_patient_hash(
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first_name=first_name,
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last_name=last_name,
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dob=dob,
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center=center.name, # Use center name
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salt=salt,
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)
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return sha256(hash_str.encode()).hexdigest()
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def calculate_examination_hash(instance: "SensitiveMeta", salt: str = SECRET_SALT) -> str:
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"""Calculates the examination hash for the instance."""
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dob = instance.patient_dob
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first_name = instance.patient_first_name
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last_name = instance.patient_last_name
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examination_date = instance.examination_date
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center = instance.center
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if not dob:
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raise ValueError("Patient DOB is required to calculate examination hash.")
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if not examination_date:
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raise ValueError("Examination date is required to calculate examination hash.")
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if not center:
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raise ValueError("Center is required to calculate examination hash.")
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hash_str = get_patient_examination_hash(
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first_name=first_name,
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last_name=last_name,
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dob=dob,
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examination_date=examination_date,
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center=center.name, # Use center name
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salt=salt,
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)
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return sha256(hash_str.encode()).hexdigest()
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def create_pseudo_examiner_logic(instance: "SensitiveMeta") -> "Examiner":
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"""Creates or retrieves the pseudo examiner based on instance data."""
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first_name = instance.examiner_first_name
|
|
205
|
+
last_name = instance.examiner_last_name
|
|
206
|
+
center = instance.center # Should be set before calling save
|
|
207
|
+
|
|
208
|
+
if not first_name or not last_name or not center:
|
|
209
|
+
logger.warning(f"Incomplete examiner info for SensitiveMeta (pk={instance.pk or 'new'}). Using default examiner.")
|
|
210
|
+
# Ensure default center exists or handle appropriately
|
|
211
|
+
try:
|
|
212
|
+
default_center = Center.objects.get_by_natural_key("endoreg_db_demo")
|
|
213
|
+
except Center.DoesNotExist:
|
|
214
|
+
logger.error("Default center 'endoreg_db_demo' not found. Cannot create default examiner.")
|
|
215
|
+
raise ValueError("Default center 'endoreg_db_demo' not found.")
|
|
216
|
+
|
|
217
|
+
examiner, _created = Examiner.custom_get_or_create(first_name="Unknown", last_name="Unknown", center=default_center)
|
|
218
|
+
else:
|
|
219
|
+
examiner, _created = Examiner.custom_get_or_create(first_name=first_name, last_name=last_name, center=center)
|
|
220
|
+
|
|
221
|
+
return examiner
|
|
222
|
+
|
|
223
|
+
|
|
224
|
+
def get_or_create_pseudo_patient_logic(instance: "SensitiveMeta") -> "Patient":
|
|
225
|
+
"""Gets or creates the pseudo patient based on instance data."""
|
|
226
|
+
# Ensure necessary fields are set
|
|
227
|
+
if not instance.patient_hash:
|
|
228
|
+
instance.patient_hash = calculate_patient_hash(instance)
|
|
229
|
+
if not instance.center:
|
|
230
|
+
raise ValueError("Center must be set before creating pseudo patient.")
|
|
231
|
+
if not instance.patient_gender:
|
|
232
|
+
raise ValueError("Patient gender must be set before creating pseudo patient.")
|
|
233
|
+
if not instance.patient_dob:
|
|
234
|
+
raise ValueError("Patient DOB must be set before creating pseudo patient.")
|
|
235
|
+
|
|
236
|
+
dob = instance.patient_dob
|
|
237
|
+
year = dob.year
|
|
238
|
+
month = dob.month
|
|
239
|
+
|
|
240
|
+
patient, _created = Patient.get_or_create_pseudo_patient_by_hash(
|
|
241
|
+
patient_hash=instance.patient_hash,
|
|
242
|
+
center=instance.center,
|
|
243
|
+
gender=instance.patient_gender,
|
|
244
|
+
birth_year=year,
|
|
245
|
+
birth_month=month,
|
|
246
|
+
)
|
|
247
|
+
return patient
|
|
248
|
+
|
|
249
|
+
|
|
250
|
+
def get_or_create_pseudo_patient_examination_logic(
|
|
251
|
+
instance: "SensitiveMeta",
|
|
252
|
+
) -> "PatientExamination":
|
|
253
|
+
"""Gets or creates the pseudo patient examination based on instance data."""
|
|
254
|
+
# Ensure necessary fields are set
|
|
255
|
+
if not instance.patient_hash:
|
|
256
|
+
instance.patient_hash = calculate_patient_hash(instance)
|
|
257
|
+
if not instance.examination_hash:
|
|
258
|
+
instance.examination_hash = calculate_examination_hash(instance)
|
|
259
|
+
|
|
260
|
+
# Ensure the pseudo patient exists first, as PatientExamination might depend on it
|
|
261
|
+
if not instance.pseudo_patient_id:
|
|
262
|
+
pseudo_patient = get_or_create_pseudo_patient_logic(instance)
|
|
263
|
+
instance.pseudo_patient_id = pseudo_patient.pk # Assign FK directly
|
|
264
|
+
|
|
265
|
+
patient_examination, _created = PatientExamination.get_or_create_pseudo_patient_examination_by_hash(
|
|
266
|
+
patient_hash=instance.patient_hash,
|
|
267
|
+
examination_hash=instance.examination_hash,
|
|
268
|
+
# Optionally pass pseudo_patient if the method requires it
|
|
269
|
+
# pseudo_patient=instance.pseudo_patient
|
|
270
|
+
)
|
|
271
|
+
return patient_examination
|
|
272
|
+
|
|
273
|
+
|
|
274
|
+
@transaction.atomic # Ensure all operations within save succeed or fail together
|
|
275
|
+
def perform_save_logic(instance: "SensitiveMeta") -> "Examiner":
|
|
276
|
+
"""
|
|
277
|
+
Contains the core logic for preparing a SensitiveMeta instance for saving.
|
|
278
|
+
Handles data generation (dates), hash calculation, and linking pseudo-entities.
|
|
279
|
+
Returns the Examiner instance to be linked via M2M after the main save.
|
|
280
|
+
"""
|
|
281
|
+
|
|
282
|
+
# --- Pre-Save Checks and Data Generation ---
|
|
283
|
+
|
|
284
|
+
# 1. Ensure DOB and Examination Date exist
|
|
285
|
+
if not instance.patient_dob:
|
|
286
|
+
logger.debug(f"SensitiveMeta (pk={instance.pk or 'new'}): Patient DOB missing, generating random.")
|
|
287
|
+
instance.patient_dob = generate_random_dob()
|
|
288
|
+
if not instance.examination_date:
|
|
289
|
+
logger.debug(f"SensitiveMeta (pk={instance.pk or 'new'}): Examination date missing, generating random.")
|
|
290
|
+
instance.examination_date = generate_random_examination_date()
|
|
291
|
+
|
|
292
|
+
# 2. Ensure Center exists (should be set before calling save)
|
|
293
|
+
if not instance.center:
|
|
294
|
+
raise ValueError("Center must be set before saving SensitiveMeta.")
|
|
295
|
+
|
|
296
|
+
# 3. Ensure Gender exists (should be set before calling save, e.g., during creation/update)
|
|
297
|
+
if not instance.patient_gender:
|
|
298
|
+
# Attempt to guess if names are available
|
|
299
|
+
first_name = instance.patient_first_name or DEFAULT_UNKNOWN_NAME
|
|
300
|
+
gender = guess_name_gender(first_name)
|
|
301
|
+
if not gender:
|
|
302
|
+
raise ValueError("Patient gender could not be determined and must be set before saving.")
|
|
303
|
+
instance.patient_gender = gender
|
|
304
|
+
|
|
305
|
+
# 4. Calculate Hashes (depends on DOB, Exam Date, Center, Names)
|
|
306
|
+
instance.patient_hash = calculate_patient_hash(instance)
|
|
307
|
+
instance.examination_hash = calculate_examination_hash(instance)
|
|
308
|
+
|
|
309
|
+
# 5. Get or Create Pseudo Patient (depends on hash, center, gender, dob)
|
|
310
|
+
# Assign directly to the FK field to avoid premature saving issues
|
|
311
|
+
pseudo_patient = get_or_create_pseudo_patient_logic(instance)
|
|
312
|
+
instance.pseudo_patient_id = pseudo_patient.pk
|
|
313
|
+
|
|
314
|
+
# 6. Get or Create Pseudo Examination (depends on hashes)
|
|
315
|
+
# Assign directly to the FK field
|
|
316
|
+
pseudo_examination = get_or_create_pseudo_patient_examination_logic(instance)
|
|
317
|
+
instance.pseudo_examination_id = pseudo_examination.pk
|
|
318
|
+
|
|
319
|
+
# 7. Get or Create Pseudo Examiner (depends on names, center)
|
|
320
|
+
# This needs to happen *after* the main instance has a PK for M2M linking.
|
|
321
|
+
# We create/get it here and return it to the main save method.
|
|
322
|
+
examiner_instance = create_pseudo_examiner_logic(instance)
|
|
323
|
+
|
|
324
|
+
# 8. Ensure SensitiveMetaState exists (will be checked/created *after* main save)
|
|
325
|
+
|
|
326
|
+
# Return the examiner instance so the model's save method can handle M2M linking
|
|
327
|
+
return examiner_instance
|
|
328
|
+
|
|
329
|
+
|
|
330
|
+
def create_sensitive_meta_from_dict(cls: Type["SensitiveMeta"], data: Dict[str, Any]) -> "SensitiveMeta":
|
|
331
|
+
"""Logic to create a SensitiveMeta instance from a dictionary."""
|
|
332
|
+
|
|
333
|
+
field_names = {f.name for f in cls._meta.get_fields() if not f.is_relation or f.one_to_one or (f.many_to_one and f.related_model)}
|
|
334
|
+
selected_data = {k: v for k, v in data.items() if k in field_names}
|
|
335
|
+
|
|
336
|
+
# --- Convert patient_dob if it's a date object ---
|
|
337
|
+
dob = selected_data.get("patient_dob")
|
|
338
|
+
if isinstance(dob, date) and not isinstance(dob, datetime):
|
|
339
|
+
# Convert date to datetime at the start of the day and make it timezone-aware
|
|
340
|
+
aware_dob = timezone.make_aware(datetime.combine(dob, datetime.min.time()))
|
|
341
|
+
selected_data["patient_dob"] = aware_dob
|
|
342
|
+
logger.debug("Converted patient_dob from date to aware datetime: %s", aware_dob)
|
|
343
|
+
elif isinstance(dob, str):
|
|
344
|
+
# Handle string DOB - check if it's a field name or actual date
|
|
345
|
+
if dob == "patient_dob" or dob in [
|
|
346
|
+
"patient_first_name",
|
|
347
|
+
"patient_last_name",
|
|
348
|
+
"examination_date",
|
|
349
|
+
]:
|
|
350
|
+
logger.warning(
|
|
351
|
+
"Skipping invalid patient_dob value '%s' - appears to be field name",
|
|
352
|
+
dob,
|
|
353
|
+
)
|
|
354
|
+
selected_data.pop("patient_dob", None) # Remove invalid value
|
|
355
|
+
else:
|
|
356
|
+
# Try to parse as date string
|
|
357
|
+
try:
|
|
358
|
+
import dateparser
|
|
359
|
+
|
|
360
|
+
parsed_dob = dateparser.parse(dob, languages=["de"], settings={"DATE_ORDER": "DMY"})
|
|
361
|
+
if parsed_dob:
|
|
362
|
+
aware_dob = timezone.make_aware(parsed_dob.replace(hour=0, minute=0, second=0, microsecond=0))
|
|
363
|
+
selected_data["patient_dob"] = aware_dob
|
|
364
|
+
logger.debug(
|
|
365
|
+
"Parsed string patient_dob '%s' to aware datetime: %s",
|
|
366
|
+
dob,
|
|
367
|
+
aware_dob,
|
|
368
|
+
)
|
|
369
|
+
else:
|
|
370
|
+
logger.warning(
|
|
371
|
+
"Could not parse patient_dob string '%s', removing from data",
|
|
372
|
+
dob,
|
|
373
|
+
)
|
|
374
|
+
selected_data.pop("patient_dob", None)
|
|
375
|
+
except Exception as e:
|
|
376
|
+
logger.warning(
|
|
377
|
+
"Error parsing patient_dob string '%s': %s, removing from data",
|
|
378
|
+
dob,
|
|
379
|
+
e,
|
|
380
|
+
)
|
|
381
|
+
selected_data.pop("patient_dob", None)
|
|
382
|
+
# --- End Conversion ---
|
|
383
|
+
|
|
384
|
+
# Similar validation for examination_date
|
|
385
|
+
exam_date = selected_data.get("examination_date")
|
|
386
|
+
if isinstance(exam_date, str):
|
|
387
|
+
if exam_date == "examination_date" or exam_date in [
|
|
388
|
+
"patient_first_name",
|
|
389
|
+
"patient_last_name",
|
|
390
|
+
"patient_dob",
|
|
391
|
+
]:
|
|
392
|
+
logger.warning(
|
|
393
|
+
"Skipping invalid examination_date value '%s' - appears to be field name",
|
|
394
|
+
exam_date,
|
|
395
|
+
)
|
|
396
|
+
selected_data.pop("examination_date", None)
|
|
397
|
+
else:
|
|
398
|
+
# Try to parse as date string
|
|
399
|
+
try:
|
|
400
|
+
# First try simple ISO format for YYYY-MM-DD
|
|
401
|
+
if len(exam_date) == 10 and exam_date.count("-") == 2:
|
|
402
|
+
try:
|
|
403
|
+
from datetime import datetime as dt
|
|
404
|
+
|
|
405
|
+
parsed_date = dt.strptime(exam_date, "%Y-%m-%d").date()
|
|
406
|
+
selected_data["examination_date"] = parsed_date
|
|
407
|
+
logger.debug(
|
|
408
|
+
"Parsed ISO examination_date '%s' to date: %s",
|
|
409
|
+
exam_date,
|
|
410
|
+
parsed_date,
|
|
411
|
+
)
|
|
412
|
+
except ValueError:
|
|
413
|
+
# Fall back to dateparser for complex formats
|
|
414
|
+
import dateparser
|
|
415
|
+
|
|
416
|
+
parsed_date = dateparser.parse(exam_date, languages=["de"], settings={"DATE_ORDER": "DMY"})
|
|
417
|
+
if parsed_date:
|
|
418
|
+
selected_data["examination_date"] = parsed_date.date()
|
|
419
|
+
logger.debug(
|
|
420
|
+
"Parsed string examination_date '%s' to date: %s",
|
|
421
|
+
exam_date,
|
|
422
|
+
parsed_date.date(),
|
|
423
|
+
)
|
|
424
|
+
else:
|
|
425
|
+
logger.warning(
|
|
426
|
+
"Could not parse examination_date string '%s', removing from data",
|
|
427
|
+
exam_date,
|
|
428
|
+
)
|
|
429
|
+
selected_data.pop("examination_date", None)
|
|
430
|
+
else:
|
|
431
|
+
# Use dateparser for non-ISO formats
|
|
432
|
+
import dateparser
|
|
433
|
+
|
|
434
|
+
parsed_date = dateparser.parse(exam_date, languages=["de"], settings={"DATE_ORDER": "DMY"})
|
|
435
|
+
if parsed_date:
|
|
436
|
+
selected_data["examination_date"] = parsed_date.date()
|
|
437
|
+
logger.debug(
|
|
438
|
+
"Parsed string examination_date '%s' to date: %s",
|
|
439
|
+
exam_date,
|
|
440
|
+
parsed_date.date(),
|
|
441
|
+
)
|
|
442
|
+
else:
|
|
443
|
+
logger.warning(
|
|
444
|
+
"Could not parse examination_date string '%s', removing from data",
|
|
445
|
+
exam_date,
|
|
446
|
+
)
|
|
447
|
+
selected_data.pop("examination_date", None)
|
|
448
|
+
except Exception as e:
|
|
449
|
+
logger.warning(
|
|
450
|
+
"Error parsing examination_date string '%s': %s, removing from data",
|
|
451
|
+
exam_date,
|
|
452
|
+
e,
|
|
453
|
+
)
|
|
454
|
+
selected_data.pop("examination_date", None)
|
|
455
|
+
|
|
456
|
+
# Handle Center
|
|
457
|
+
center_name = data.get("center_name")
|
|
458
|
+
if not center_name:
|
|
459
|
+
raise ValueError("center_name is required in data dictionary.")
|
|
460
|
+
try:
|
|
461
|
+
center = Center.objects.get_by_natural_key(center_name)
|
|
462
|
+
selected_data["center"] = center
|
|
463
|
+
except Center.DoesNotExist as exc:
|
|
464
|
+
raise ValueError(f"Center with name '{center_name}' does not exist.") from exc
|
|
465
|
+
|
|
466
|
+
# Handle Names and Gender
|
|
467
|
+
first_name = selected_data.get("patient_first_name") or DEFAULT_UNKNOWN_NAME
|
|
468
|
+
last_name = selected_data.get("patient_last_name") or DEFAULT_UNKNOWN_NAME
|
|
469
|
+
selected_data["patient_first_name"] = first_name # Ensure defaults are set
|
|
470
|
+
selected_data["patient_last_name"] = last_name
|
|
471
|
+
|
|
472
|
+
patient_gender_input = selected_data.get("patient_gender")
|
|
473
|
+
|
|
474
|
+
if isinstance(patient_gender_input, Gender):
|
|
475
|
+
# Already a Gender object, nothing to do
|
|
476
|
+
pass
|
|
477
|
+
elif isinstance(patient_gender_input, str):
|
|
478
|
+
# Input is a string (gender name)
|
|
479
|
+
try:
|
|
480
|
+
selected_data["patient_gender"] = Gender.objects.get(name=patient_gender_input)
|
|
481
|
+
except Gender.DoesNotExist:
|
|
482
|
+
logger.warning(f"Gender with name '{patient_gender_input}' provided but not found. Attempting to guess or use default.")
|
|
483
|
+
# Fall through to guessing logic if provided string name is invalid
|
|
484
|
+
patient_gender_input = None # Reset to trigger guessing
|
|
485
|
+
|
|
486
|
+
if not isinstance(selected_data.get("patient_gender"), Gender): # If not already a Gender object (e.g. was None, or string lookup failed)
|
|
487
|
+
gender_name_to_use = guess_name_gender(first_name)
|
|
488
|
+
if not gender_name_to_use:
|
|
489
|
+
logger.warning(f"Could not guess gender for name '{first_name}'. Setting Gender to unknown.")
|
|
490
|
+
gender_name_to_use = "unknown"
|
|
491
|
+
try:
|
|
492
|
+
selected_data["patient_gender"] = Gender.objects.get(name=gender_name_to_use)
|
|
493
|
+
except Gender.DoesNotExist:
|
|
494
|
+
# This should ideally not happen if "unknown" gender is guaranteed to exist
|
|
495
|
+
raise ValueError(f"Default or guessed gender '{gender_name_to_use}' does not exist in Gender table.")
|
|
496
|
+
|
|
497
|
+
# Update name DB
|
|
498
|
+
update_name_db(first_name, last_name)
|
|
499
|
+
|
|
500
|
+
# Instantiate without saving yet
|
|
501
|
+
sensitive_meta = cls(**selected_data)
|
|
502
|
+
|
|
503
|
+
# Call save once at the end. This triggers the custom save logic.
|
|
504
|
+
sensitive_meta.save() # This will call perform_save_logic internally
|
|
505
|
+
|
|
506
|
+
return sensitive_meta
|
|
507
|
+
|
|
508
|
+
|
|
509
|
+
def update_sensitive_meta_from_dict(instance: "SensitiveMeta", data: Dict[str, Any]) -> "SensitiveMeta":
|
|
510
|
+
"""Logic to update a SensitiveMeta instance from a dictionary."""
|
|
511
|
+
field_names = {f.name for f in instance._meta.get_fields() if not f.is_relation or f.one_to_one or (f.many_to_one and f.related_model)}
|
|
512
|
+
# Exclude FKs that should not be updated directly from dict keys (handled separately or via save logic)
|
|
513
|
+
excluded_fields = {"pseudo_patient", "pseudo_examination"}
|
|
514
|
+
selected_data = {k: v for k, v in data.items() if k in field_names and k not in excluded_fields}
|
|
515
|
+
|
|
516
|
+
# Handle potential Center update
|
|
517
|
+
center_name = data.get("center_name")
|
|
518
|
+
if center_name:
|
|
519
|
+
try:
|
|
520
|
+
center = Center.objects.get_by_natural_key(center_name)
|
|
521
|
+
instance.center = center # Update center directly
|
|
522
|
+
except Center.DoesNotExist as exc:
|
|
523
|
+
logger.warning(f"Center '{center_name}' not found during update. Keeping existing center.")
|
|
524
|
+
selected_data.pop("center", None) # Remove from dict if not found
|
|
525
|
+
|
|
526
|
+
# Set examiner names if provided, before calling save
|
|
527
|
+
examiner_first_name = data.get("examiner_first_name")
|
|
528
|
+
examiner_last_name = data.get("examiner_last_name")
|
|
529
|
+
if examiner_first_name is not None: # Allow setting empty strings
|
|
530
|
+
instance.examiner_first_name = examiner_first_name
|
|
531
|
+
if examiner_last_name is not None:
|
|
532
|
+
instance.examiner_last_name = examiner_last_name
|
|
533
|
+
|
|
534
|
+
# Handle patient_gender specially with graceful error handling
|
|
535
|
+
patient_gender_input = data.get("patient_gender")
|
|
536
|
+
if patient_gender_input is not None:
|
|
537
|
+
try:
|
|
538
|
+
if isinstance(patient_gender_input, Gender):
|
|
539
|
+
selected_data["patient_gender"] = patient_gender_input
|
|
540
|
+
elif isinstance(patient_gender_input, str):
|
|
541
|
+
gender_input_clean = patient_gender_input.strip()
|
|
542
|
+
# Try direct case-insensitive DB lookup first
|
|
543
|
+
gender_obj = Gender.objects.filter(name__iexact=gender_input_clean).first()
|
|
544
|
+
if gender_obj:
|
|
545
|
+
selected_data["patient_gender"] = gender_obj
|
|
546
|
+
logger.debug(f"Successfully matched gender string '{patient_gender_input}' to Gender object via iexact lookup")
|
|
547
|
+
else:
|
|
548
|
+
# Use mapping helper for fallback
|
|
549
|
+
mapped = _map_gender_string_to_standard(gender_input_clean)
|
|
550
|
+
if mapped:
|
|
551
|
+
gender_obj = Gender.objects.filter(name__iexact=mapped).first()
|
|
552
|
+
if gender_obj:
|
|
553
|
+
selected_data["patient_gender"] = gender_obj
|
|
554
|
+
logger.info(f"Mapped gender '{patient_gender_input}' to '{mapped}' via fallback mapping")
|
|
555
|
+
else:
|
|
556
|
+
logger.warning(f"Mapped gender '{patient_gender_input}' to '{mapped}', but no such Gender in DB. Trying 'unknown'.")
|
|
557
|
+
unknown_gender = Gender.objects.filter(name__iexact="unknown").first()
|
|
558
|
+
if unknown_gender:
|
|
559
|
+
selected_data["patient_gender"] = unknown_gender
|
|
560
|
+
logger.warning(f"Using 'unknown' gender as fallback for '{patient_gender_input}'")
|
|
561
|
+
else:
|
|
562
|
+
logger.error(f"No 'unknown' gender found in database. Cannot handle gender '{patient_gender_input}'. Skipping gender update.")
|
|
563
|
+
selected_data.pop("patient_gender", None)
|
|
564
|
+
else:
|
|
565
|
+
# Last resort: try to get 'unknown' gender
|
|
566
|
+
unknown_gender = Gender.objects.filter(name__iexact="unknown").first()
|
|
567
|
+
if unknown_gender:
|
|
568
|
+
selected_data["patient_gender"] = unknown_gender
|
|
569
|
+
logger.warning(f"Using 'unknown' gender as fallback for '{patient_gender_input}' (no mapping)")
|
|
570
|
+
else:
|
|
571
|
+
logger.error(f"No 'unknown' gender found in database. Cannot handle gender '{patient_gender_input}'. Skipping gender update.")
|
|
572
|
+
selected_data.pop("patient_gender", None)
|
|
573
|
+
else:
|
|
574
|
+
logger.warning(f"Unexpected patient_gender type {type(patient_gender_input)}: {patient_gender_input}. Skipping gender update.")
|
|
575
|
+
selected_data.pop("patient_gender", None)
|
|
576
|
+
except Exception as e:
|
|
577
|
+
logger.exception(f"Error handling patient_gender '{patient_gender_input}': {e}. Skipping gender update.")
|
|
578
|
+
selected_data.pop("patient_gender", None)
|
|
579
|
+
|
|
580
|
+
# Update other attributes from selected_data
|
|
581
|
+
patient_name_changed = False
|
|
582
|
+
for k, v in selected_data.items():
|
|
583
|
+
# Avoid overwriting examiner names if they were just explicitly set
|
|
584
|
+
if (
|
|
585
|
+
k not in ["examiner_first_name", "examiner_last_name"]
|
|
586
|
+
or (k == "examiner_first_name" and examiner_first_name is None)
|
|
587
|
+
or (k == "examiner_last_name" and examiner_last_name is None)
|
|
588
|
+
):
|
|
589
|
+
try:
|
|
590
|
+
# --- Convert patient_dob if it's a date object ---
|
|
591
|
+
value_to_set = v
|
|
592
|
+
if k == "patient_dob":
|
|
593
|
+
if isinstance(v, date) and not isinstance(v, datetime):
|
|
594
|
+
aware_dob = timezone.make_aware(datetime.combine(v, datetime.min.time()))
|
|
595
|
+
value_to_set = aware_dob
|
|
596
|
+
logger.debug(
|
|
597
|
+
"Converted patient_dob from date to aware datetime during update: %s",
|
|
598
|
+
aware_dob,
|
|
599
|
+
)
|
|
600
|
+
elif isinstance(v, str):
|
|
601
|
+
# Handle string DOB - check if it's a field name or actual date
|
|
602
|
+
if v == "patient_dob" or v in [
|
|
603
|
+
"patient_first_name",
|
|
604
|
+
"patient_last_name",
|
|
605
|
+
"examination_date",
|
|
606
|
+
]:
|
|
607
|
+
logger.warning(
|
|
608
|
+
"Skipping invalid patient_dob value '%s' during update - appears to be field name",
|
|
609
|
+
v,
|
|
610
|
+
)
|
|
611
|
+
continue # Skip this field
|
|
612
|
+
else:
|
|
613
|
+
# Try to parse as date string
|
|
614
|
+
try:
|
|
615
|
+
import dateparser
|
|
616
|
+
|
|
617
|
+
parsed_dob = dateparser.parse(v, languages=["de"], settings={"DATE_ORDER": "DMY"})
|
|
618
|
+
if parsed_dob:
|
|
619
|
+
value_to_set = timezone.make_aware(parsed_dob.replace(hour=0, minute=0, second=0, microsecond=0))
|
|
620
|
+
logger.debug(
|
|
621
|
+
"Parsed string patient_dob '%s' during update to aware datetime: %s",
|
|
622
|
+
v,
|
|
623
|
+
value_to_set,
|
|
624
|
+
)
|
|
625
|
+
else:
|
|
626
|
+
logger.warning(
|
|
627
|
+
"Could not parse patient_dob string '%s' during update, skipping",
|
|
628
|
+
v,
|
|
629
|
+
)
|
|
630
|
+
continue
|
|
631
|
+
except Exception as e:
|
|
632
|
+
logger.warning(
|
|
633
|
+
"Error parsing patient_dob string '%s' during update: %s, skipping",
|
|
634
|
+
v,
|
|
635
|
+
e,
|
|
636
|
+
)
|
|
637
|
+
continue
|
|
638
|
+
elif k == "examination_date" and isinstance(v, str):
|
|
639
|
+
if v == "examination_date" or v in [
|
|
640
|
+
"patient_first_name",
|
|
641
|
+
"patient_last_name",
|
|
642
|
+
"patient_dob",
|
|
643
|
+
]:
|
|
644
|
+
logger.warning(
|
|
645
|
+
"Skipping invalid examination_date value '%s' during update - appears to be field name",
|
|
646
|
+
v,
|
|
647
|
+
)
|
|
648
|
+
continue
|
|
649
|
+
else:
|
|
650
|
+
# Try to parse as date string
|
|
651
|
+
try:
|
|
652
|
+
import dateparser
|
|
653
|
+
|
|
654
|
+
parsed_date = dateparser.parse(v, languages=["de"], settings={"DATE_ORDER": "DMY"})
|
|
655
|
+
if parsed_date:
|
|
656
|
+
value_to_set = parsed_date.date()
|
|
657
|
+
logger.debug(
|
|
658
|
+
"Parsed string examination_date '%s' during update to date: %s",
|
|
659
|
+
v,
|
|
660
|
+
value_to_set,
|
|
661
|
+
)
|
|
662
|
+
else:
|
|
663
|
+
logger.warning(
|
|
664
|
+
"Could not parse examination_date string '%s' during update, skipping",
|
|
665
|
+
v,
|
|
666
|
+
)
|
|
667
|
+
continue
|
|
668
|
+
except Exception as e:
|
|
669
|
+
logger.warning(
|
|
670
|
+
"Error parsing examination_date string '%s' during update: %s, skipping",
|
|
671
|
+
v,
|
|
672
|
+
e,
|
|
673
|
+
)
|
|
674
|
+
continue
|
|
675
|
+
# --- End Conversion ---
|
|
676
|
+
|
|
677
|
+
# Check if patient name is changing
|
|
678
|
+
if k in ["patient_first_name", "patient_last_name"] and getattr(instance, k) != value_to_set:
|
|
679
|
+
patient_name_changed = True
|
|
680
|
+
|
|
681
|
+
setattr(instance, k, value_to_set) # Use value_to_set
|
|
682
|
+
|
|
683
|
+
except Exception as e:
|
|
684
|
+
logger.error(f"Error setting attribute '{k}' to '{v}': {e}. Skipping this field.")
|
|
685
|
+
continue
|
|
686
|
+
|
|
687
|
+
# Update name DB if patient names changed
|
|
688
|
+
if patient_name_changed:
|
|
689
|
+
try:
|
|
690
|
+
update_name_db(instance.patient_first_name, instance.patient_last_name)
|
|
691
|
+
except Exception as e:
|
|
692
|
+
logger.warning(f"Error updating name database: {e}")
|
|
693
|
+
|
|
694
|
+
# Call save - this will trigger the full save logic including hash recalculation etc.
|
|
695
|
+
try:
|
|
696
|
+
instance.save()
|
|
697
|
+
except Exception as e:
|
|
698
|
+
logger.error(f"Error saving SensitiveMeta instance: {e}")
|
|
699
|
+
raise
|
|
700
|
+
|
|
701
|
+
return instance
|
|
702
|
+
|
|
703
|
+
|
|
704
|
+
def update_or_create_sensitive_meta_from_dict(
|
|
705
|
+
cls: Type["SensitiveMeta"],
|
|
706
|
+
data: Dict[str, Any],
|
|
707
|
+
instance: Optional["SensitiveMeta"] = None,
|
|
708
|
+
) -> "SensitiveMeta":
|
|
709
|
+
"""Logic to update or create a SensitiveMeta instance from a dictionary."""
|
|
710
|
+
# Check if the instance already exists based on unique fields
|
|
711
|
+
if instance:
|
|
712
|
+
# Update the existing instance
|
|
713
|
+
return update_sensitive_meta_from_dict(instance, data), False
|
|
714
|
+
else:
|
|
715
|
+
# Create a new instance
|
|
716
|
+
return create_sensitive_meta_from_dict(cls, data), True
|
|
717
|
+
|
|
718
|
+
|
|
719
|
+
def _map_gender_string_to_standard(gender_str: str) -> Optional[str]:
|
|
720
|
+
"""Maps various gender string inputs to standard gender names used in the DB."""
|
|
721
|
+
mapping = {
|
|
722
|
+
"male": ["male", "m", "männlich", "man"],
|
|
723
|
+
"female": ["female", "f", "weiblich", "woman"],
|
|
724
|
+
"unknown": ["unknown", "unbekannt", "other", "diverse", ""],
|
|
725
|
+
}
|
|
726
|
+
gender_lower = gender_str.strip().lower()
|
|
727
|
+
for standard, variants in mapping.items():
|
|
728
|
+
if gender_lower in variants:
|
|
729
|
+
return standard
|
|
730
|
+
return None
|