endoreg-db 0.8.8.9__py3-none-any.whl → 0.8.9.10__py3-none-any.whl
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- endoreg_db/admin.py +10 -5
- endoreg_db/apps.py +4 -7
- endoreg_db/authz/auth.py +1 -0
- endoreg_db/authz/backends.py +1 -1
- endoreg_db/authz/management/commands/list_routes.py +2 -0
- endoreg_db/authz/middleware.py +8 -7
- endoreg_db/authz/permissions.py +21 -10
- endoreg_db/authz/policy.py +14 -19
- endoreg_db/authz/views_auth.py +14 -10
- endoreg_db/codemods/rename_datetime_fields.py +8 -1
- endoreg_db/exceptions.py +5 -2
- endoreg_db/forms/__init__.py +0 -1
- endoreg_db/forms/examination_form.py +4 -3
- endoreg_db/forms/patient_finding_intervention_form.py +30 -8
- endoreg_db/forms/patient_form.py +9 -13
- endoreg_db/forms/questionnaires/__init__.py +1 -1
- endoreg_db/forms/settings/__init__.py +4 -1
- endoreg_db/forms/unit.py +2 -1
- endoreg_db/helpers/count_db.py +17 -14
- endoreg_db/helpers/default_objects.py +2 -1
- endoreg_db/helpers/download_segmentation_model.py +4 -3
- endoreg_db/helpers/interact.py +0 -5
- endoreg_db/helpers/test_video_helper.py +33 -25
- endoreg_db/import_files/__init__.py +1 -1
- endoreg_db/import_files/context/__init__.py +1 -1
- endoreg_db/import_files/context/default_sensitive_meta.py +11 -9
- endoreg_db/import_files/context/ensure_center.py +4 -4
- endoreg_db/import_files/context/file_lock.py +3 -3
- endoreg_db/import_files/context/import_context.py +11 -12
- endoreg_db/import_files/context/validate_directories.py +1 -0
- endoreg_db/import_files/file_storage/create_report_file.py +57 -34
- endoreg_db/import_files/file_storage/create_video_file.py +64 -35
- endoreg_db/import_files/file_storage/sensitive_meta_storage.py +5 -2
- endoreg_db/import_files/file_storage/state_management.py +146 -83
- endoreg_db/import_files/file_storage/storage.py +5 -1
- endoreg_db/import_files/processing/report_processing/report_anonymization.py +24 -19
- endoreg_db/import_files/processing/sensitive_meta_adapter.py +3 -3
- endoreg_db/import_files/processing/video_processing/video_anonymization.py +18 -18
- endoreg_db/import_files/pseudonymization/k_anonymity.py +8 -9
- endoreg_db/import_files/pseudonymization/k_pseudonymity.py +16 -5
- endoreg_db/import_files/report_import_service.py +36 -30
- endoreg_db/import_files/video_import_service.py +27 -23
- endoreg_db/logger_conf.py +56 -40
- endoreg_db/management/__init__.py +1 -1
- endoreg_db/management/commands/__init__.py +1 -1
- endoreg_db/management/commands/check_auth.py +45 -38
- endoreg_db/management/commands/create_model_meta_from_huggingface.py +53 -2
- endoreg_db/management/commands/create_multilabel_model_meta.py +54 -19
- endoreg_db/management/commands/fix_missing_patient_data.py +105 -71
- endoreg_db/management/commands/fix_video_paths.py +75 -54
- endoreg_db/management/commands/import_report.py +1 -3
- endoreg_db/management/commands/list_routes.py +2 -0
- endoreg_db/management/commands/load_ai_model_data.py +8 -2
- endoreg_db/management/commands/load_ai_model_label_data.py +0 -1
- endoreg_db/management/commands/load_center_data.py +3 -3
- endoreg_db/management/commands/load_distribution_data.py +35 -38
- endoreg_db/management/commands/load_endoscope_data.py +0 -3
- endoreg_db/management/commands/load_examination_data.py +20 -4
- endoreg_db/management/commands/load_finding_data.py +18 -3
- endoreg_db/management/commands/load_gender_data.py +17 -24
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +95 -85
- endoreg_db/management/commands/load_information_source.py +0 -3
- endoreg_db/management/commands/load_lab_value_data.py +14 -3
- endoreg_db/management/commands/load_legacy_data.py +303 -0
- endoreg_db/management/commands/load_name_data.py +1 -2
- endoreg_db/management/commands/load_pdf_type_data.py +4 -8
- endoreg_db/management/commands/load_profession_data.py +0 -1
- endoreg_db/management/commands/load_report_reader_flag_data.py +0 -4
- endoreg_db/management/commands/load_requirement_data.py +6 -2
- endoreg_db/management/commands/load_unit_data.py +0 -4
- endoreg_db/management/commands/load_user_groups.py +5 -7
- endoreg_db/management/commands/model_input.py +169 -0
- endoreg_db/management/commands/register_ai_model.py +22 -16
- endoreg_db/management/commands/setup_endoreg_db.py +110 -32
- endoreg_db/management/commands/storage_management.py +14 -8
- endoreg_db/management/commands/summarize_db_content.py +154 -63
- endoreg_db/management/commands/train_image_multilabel_model.py +144 -0
- endoreg_db/management/commands/validate_video_files.py +82 -50
- endoreg_db/management/commands/video_validation.py +4 -6
- endoreg_db/migrations/0001_initial.py +112 -63
- endoreg_db/migrations/__init__.py +0 -0
- endoreg_db/models/__init__.py +8 -0
- endoreg_db/models/administration/ai/active_model.py +5 -5
- endoreg_db/models/administration/ai/ai_model.py +41 -18
- endoreg_db/models/administration/ai/model_type.py +1 -0
- endoreg_db/models/administration/case/case.py +22 -22
- endoreg_db/models/administration/center/__init__.py +5 -5
- endoreg_db/models/administration/center/center.py +6 -2
- endoreg_db/models/administration/center/center_resource.py +18 -4
- endoreg_db/models/administration/center/center_shift.py +3 -1
- endoreg_db/models/administration/center/center_waste.py +6 -2
- endoreg_db/models/administration/person/__init__.py +1 -1
- endoreg_db/models/administration/person/employee/__init__.py +1 -1
- endoreg_db/models/administration/person/employee/employee_type.py +3 -1
- endoreg_db/models/administration/person/examiner/__init__.py +1 -1
- endoreg_db/models/administration/person/examiner/examiner.py +10 -2
- endoreg_db/models/administration/person/names/first_name.py +6 -4
- endoreg_db/models/administration/person/names/last_name.py +4 -3
- endoreg_db/models/administration/person/patient/__init__.py +1 -1
- endoreg_db/models/administration/person/patient/patient.py +0 -1
- endoreg_db/models/administration/person/patient/patient_external_id.py +0 -1
- endoreg_db/models/administration/person/person.py +1 -1
- endoreg_db/models/administration/product/__init__.py +7 -6
- endoreg_db/models/administration/product/product.py +6 -2
- endoreg_db/models/administration/product/product_group.py +9 -7
- endoreg_db/models/administration/product/product_material.py +9 -2
- endoreg_db/models/administration/product/reference_product.py +64 -15
- endoreg_db/models/administration/qualification/qualification.py +3 -1
- endoreg_db/models/administration/shift/shift.py +3 -1
- endoreg_db/models/administration/shift/shift_type.py +12 -4
- endoreg_db/models/aidataset/__init__.py +5 -0
- endoreg_db/models/aidataset/aidataset.py +193 -0
- endoreg_db/models/label/__init__.py +1 -1
- endoreg_db/models/label/label.py +10 -2
- endoreg_db/models/label/label_set.py +3 -1
- endoreg_db/models/label/label_video_segment/_create_from_video.py +6 -2
- endoreg_db/models/label/label_video_segment/label_video_segment.py +148 -44
- endoreg_db/models/media/__init__.py +12 -5
- endoreg_db/models/media/frame/__init__.py +1 -1
- endoreg_db/models/media/frame/frame.py +34 -8
- endoreg_db/models/media/pdf/__init__.py +2 -1
- endoreg_db/models/media/pdf/raw_pdf.py +11 -4
- endoreg_db/models/media/pdf/report_file.py +6 -2
- endoreg_db/models/media/pdf/report_reader/__init__.py +3 -3
- endoreg_db/models/media/pdf/report_reader/report_reader_flag.py +15 -5
- endoreg_db/models/media/video/create_from_file.py +20 -41
- endoreg_db/models/media/video/pipe_1.py +75 -30
- endoreg_db/models/media/video/pipe_2.py +37 -12
- endoreg_db/models/media/video/video_file.py +36 -24
- endoreg_db/models/media/video/video_file_ai.py +235 -70
- endoreg_db/models/media/video/video_file_anonymize.py +240 -65
- endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +6 -1
- endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +3 -1
- endoreg_db/models/media/video/video_file_frames/_delete_frames.py +30 -9
- endoreg_db/models/media/video/video_file_frames/_extract_frames.py +95 -29
- endoreg_db/models/media/video/video_file_frames/_get_frame.py +13 -3
- endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +4 -1
- endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +15 -3
- endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +15 -3
- endoreg_db/models/media/video/video_file_frames/_get_frames.py +7 -2
- endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +109 -23
- endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +111 -27
- endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +46 -13
- endoreg_db/models/media/video/video_file_io.py +85 -33
- endoreg_db/models/media/video/video_file_meta/__init__.py +6 -6
- endoreg_db/models/media/video/video_file_meta/get_crop_template.py +17 -4
- endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +28 -7
- endoreg_db/models/media/video/video_file_meta/get_fps.py +46 -13
- endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +81 -20
- endoreg_db/models/media/video/video_file_meta/text_meta.py +61 -20
- endoreg_db/models/media/video/video_file_meta/video_meta.py +40 -12
- endoreg_db/models/media/video/video_file_segments.py +118 -27
- endoreg_db/models/media/video/video_metadata.py +25 -6
- endoreg_db/models/media/video/video_processing.py +54 -15
- endoreg_db/models/medical/__init__.py +3 -13
- endoreg_db/models/medical/contraindication/__init__.py +3 -1
- endoreg_db/models/medical/disease.py +18 -6
- endoreg_db/models/medical/event.py +6 -2
- endoreg_db/models/medical/examination/__init__.py +5 -1
- endoreg_db/models/medical/examination/examination.py +22 -6
- endoreg_db/models/medical/examination/examination_indication.py +23 -7
- endoreg_db/models/medical/examination/examination_time.py +6 -2
- endoreg_db/models/medical/finding/__init__.py +3 -1
- endoreg_db/models/medical/finding/finding.py +37 -12
- endoreg_db/models/medical/finding/finding_classification.py +27 -8
- endoreg_db/models/medical/finding/finding_intervention.py +19 -6
- endoreg_db/models/medical/finding/finding_type.py +3 -1
- endoreg_db/models/medical/hardware/__init__.py +1 -1
- endoreg_db/models/medical/hardware/endoscope.py +14 -2
- endoreg_db/models/medical/laboratory/__init__.py +1 -1
- endoreg_db/models/medical/laboratory/lab_value.py +139 -39
- endoreg_db/models/medical/medication/__init__.py +7 -3
- endoreg_db/models/medical/medication/medication.py +3 -1
- endoreg_db/models/medical/medication/medication_indication.py +3 -1
- endoreg_db/models/medical/medication/medication_indication_type.py +11 -3
- endoreg_db/models/medical/medication/medication_intake_time.py +3 -1
- endoreg_db/models/medical/medication/medication_schedule.py +3 -1
- endoreg_db/models/medical/patient/__init__.py +2 -10
- endoreg_db/models/medical/patient/medication_examples.py +3 -14
- endoreg_db/models/medical/patient/patient_disease.py +17 -5
- endoreg_db/models/medical/patient/patient_event.py +12 -4
- endoreg_db/models/medical/patient/patient_examination.py +52 -15
- endoreg_db/models/medical/patient/patient_examination_indication.py +15 -4
- endoreg_db/models/medical/patient/patient_finding.py +105 -29
- endoreg_db/models/medical/patient/patient_finding_classification.py +41 -12
- endoreg_db/models/medical/patient/patient_finding_intervention.py +11 -3
- endoreg_db/models/medical/patient/patient_lab_sample.py +6 -2
- endoreg_db/models/medical/patient/patient_lab_value.py +42 -10
- endoreg_db/models/medical/patient/patient_medication.py +25 -7
- endoreg_db/models/medical/patient/patient_medication_schedule.py +34 -10
- endoreg_db/models/metadata/model_meta.py +40 -12
- endoreg_db/models/metadata/model_meta_logic.py +51 -16
- endoreg_db/models/metadata/sensitive_meta.py +65 -28
- endoreg_db/models/metadata/sensitive_meta_logic.py +28 -26
- endoreg_db/models/metadata/video_meta.py +146 -39
- endoreg_db/models/metadata/video_prediction_logic.py +70 -21
- endoreg_db/models/metadata/video_prediction_meta.py +80 -27
- endoreg_db/models/operation_log.py +63 -0
- endoreg_db/models/other/__init__.py +10 -10
- endoreg_db/models/other/distribution/__init__.py +9 -7
- endoreg_db/models/other/distribution/base_value_distribution.py +3 -1
- endoreg_db/models/other/distribution/date_value_distribution.py +19 -5
- endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +3 -1
- endoreg_db/models/other/distribution/numeric_value_distribution.py +34 -9
- endoreg_db/models/other/emission/__init__.py +1 -1
- endoreg_db/models/other/emission/emission_factor.py +9 -3
- endoreg_db/models/other/information_source.py +15 -5
- endoreg_db/models/other/material.py +3 -1
- endoreg_db/models/other/transport_route.py +3 -1
- endoreg_db/models/other/unit.py +6 -2
- endoreg_db/models/report/report.py +0 -1
- endoreg_db/models/requirement/requirement.py +84 -27
- endoreg_db/models/requirement/requirement_error.py +5 -6
- endoreg_db/models/requirement/requirement_evaluation/__init__.py +1 -1
- endoreg_db/models/requirement/requirement_evaluation/evaluate_with_dependencies.py +8 -8
- endoreg_db/models/requirement/requirement_evaluation/get_values.py +3 -3
- endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +24 -8
- endoreg_db/models/requirement/requirement_operator.py +28 -8
- endoreg_db/models/requirement/requirement_set.py +34 -11
- endoreg_db/models/state/__init__.py +1 -0
- endoreg_db/models/state/audit_ledger.py +9 -2
- endoreg_db/models/{media → state}/processing_history/__init__.py +1 -3
- endoreg_db/models/state/processing_history/processing_history.py +136 -0
- endoreg_db/models/state/raw_pdf.py +0 -1
- endoreg_db/models/state/video.py +2 -3
- endoreg_db/models/utils.py +4 -2
- endoreg_db/queries/__init__.py +2 -6
- endoreg_db/queries/annotations/__init__.py +1 -3
- endoreg_db/queries/annotations/legacy.py +37 -26
- endoreg_db/root_urls.py +3 -4
- endoreg_db/schemas/examination_evaluation.py +3 -0
- endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +249 -163
- endoreg_db/serializers/__init__.py +2 -8
- endoreg_db/serializers/administration/__init__.py +1 -2
- endoreg_db/serializers/administration/ai/__init__.py +0 -1
- endoreg_db/serializers/administration/ai/active_model.py +3 -1
- endoreg_db/serializers/administration/ai/ai_model.py +5 -3
- endoreg_db/serializers/administration/ai/model_type.py +3 -1
- endoreg_db/serializers/administration/center.py +7 -2
- endoreg_db/serializers/administration/gender.py +4 -2
- endoreg_db/serializers/anonymization.py +13 -13
- endoreg_db/serializers/evaluation/examination_evaluation.py +0 -1
- endoreg_db/serializers/examination/__init__.py +1 -1
- endoreg_db/serializers/examination/base.py +12 -13
- endoreg_db/serializers/examination/dropdown.py +6 -7
- endoreg_db/serializers/examination_serializer.py +3 -6
- endoreg_db/serializers/finding/__init__.py +1 -1
- endoreg_db/serializers/finding/finding.py +14 -7
- endoreg_db/serializers/finding_classification/__init__.py +3 -3
- endoreg_db/serializers/finding_classification/choice.py +3 -3
- endoreg_db/serializers/finding_classification/classification.py +2 -4
- endoreg_db/serializers/label_video_segment/__init__.py +5 -3
- endoreg_db/serializers/{label → label_video_segment}/image_classification_annotation.py +5 -5
- endoreg_db/serializers/label_video_segment/label/__init__.py +6 -0
- endoreg_db/serializers/{label → label_video_segment/label}/label.py +1 -1
- endoreg_db/serializers/label_video_segment/label_video_segment.py +338 -228
- endoreg_db/serializers/meta/__init__.py +1 -2
- endoreg_db/serializers/meta/sensitive_meta_detail.py +28 -13
- endoreg_db/serializers/meta/sensitive_meta_update.py +51 -46
- endoreg_db/serializers/meta/sensitive_meta_verification.py +19 -16
- endoreg_db/serializers/misc/__init__.py +2 -2
- endoreg_db/serializers/misc/file_overview.py +11 -7
- endoreg_db/serializers/misc/stats.py +10 -8
- endoreg_db/serializers/misc/translatable_field_mix_in.py +6 -6
- endoreg_db/serializers/misc/upload_job.py +32 -29
- endoreg_db/serializers/patient/__init__.py +2 -1
- endoreg_db/serializers/patient/patient.py +32 -15
- endoreg_db/serializers/patient/patient_dropdown.py +11 -3
- endoreg_db/serializers/patient_examination/__init__.py +1 -1
- endoreg_db/serializers/patient_examination/patient_examination.py +67 -40
- endoreg_db/serializers/patient_finding/__init__.py +1 -1
- endoreg_db/serializers/patient_finding/patient_finding.py +2 -1
- endoreg_db/serializers/patient_finding/patient_finding_classification.py +17 -9
- endoreg_db/serializers/patient_finding/patient_finding_detail.py +26 -17
- endoreg_db/serializers/patient_finding/patient_finding_intervention.py +7 -5
- endoreg_db/serializers/patient_finding/patient_finding_list.py +10 -11
- endoreg_db/serializers/patient_finding/patient_finding_write.py +36 -27
- endoreg_db/serializers/pdf/__init__.py +1 -3
- endoreg_db/serializers/requirements/requirement_schema.py +1 -6
- endoreg_db/serializers/sensitive_meta_serializer.py +100 -81
- endoreg_db/serializers/video/__init__.py +2 -2
- endoreg_db/serializers/video/{segmentation.py → video_file.py} +66 -47
- endoreg_db/serializers/video/video_file_brief.py +6 -2
- endoreg_db/serializers/video/video_file_detail.py +36 -23
- endoreg_db/serializers/video/video_file_list.py +4 -2
- endoreg_db/serializers/video/video_processing_history.py +54 -50
- endoreg_db/services/__init__.py +1 -1
- endoreg_db/services/anonymization.py +2 -2
- endoreg_db/services/examination_evaluation.py +40 -17
- endoreg_db/services/model_meta_from_hf.py +76 -0
- endoreg_db/services/polling_coordinator.py +101 -70
- endoreg_db/services/pseudonym_service.py +27 -22
- endoreg_db/services/report_import.py +6 -3
- endoreg_db/services/segment_sync.py +75 -59
- endoreg_db/services/video_import.py +6 -7
- endoreg_db/urls/__init__.py +2 -2
- endoreg_db/urls/ai.py +7 -25
- endoreg_db/urls/anonymization.py +61 -15
- endoreg_db/urls/auth.py +4 -4
- endoreg_db/urls/classification.py +4 -9
- endoreg_db/urls/examination.py +27 -18
- endoreg_db/urls/media.py +27 -34
- endoreg_db/urls/patient.py +11 -7
- endoreg_db/urls/requirements.py +3 -1
- endoreg_db/urls/root_urls.py +2 -3
- endoreg_db/urls/stats.py +24 -16
- endoreg_db/urls/upload.py +3 -11
- endoreg_db/utils/__init__.py +14 -15
- endoreg_db/utils/ai/__init__.py +1 -1
- endoreg_db/utils/ai/data_loader_for_model_input.py +262 -0
- endoreg_db/utils/ai/data_loader_for_model_training.py +262 -0
- endoreg_db/utils/ai/get.py +2 -1
- endoreg_db/utils/ai/inference_dataset.py +14 -15
- endoreg_db/utils/ai/model_training/config.py +117 -0
- endoreg_db/utils/ai/model_training/dataset.py +74 -0
- endoreg_db/utils/ai/model_training/losses.py +68 -0
- endoreg_db/utils/ai/model_training/metrics.py +78 -0
- endoreg_db/utils/ai/model_training/model_backbones.py +155 -0
- endoreg_db/utils/ai/model_training/model_gastronet_resnet.py +118 -0
- endoreg_db/utils/ai/model_training/trainer_gastronet_multilabel.py +771 -0
- endoreg_db/utils/ai/multilabel_classification_net.py +21 -6
- endoreg_db/utils/ai/predict.py +4 -4
- endoreg_db/utils/ai/preprocess.py +19 -11
- endoreg_db/utils/calc_duration_seconds.py +4 -4
- endoreg_db/utils/case_generator/lab_sample_factory.py +3 -4
- endoreg_db/utils/check_video_files.py +74 -47
- endoreg_db/utils/cropping.py +10 -9
- endoreg_db/utils/dataloader.py +11 -3
- endoreg_db/utils/dates.py +3 -4
- endoreg_db/utils/defaults/set_default_center.py +7 -6
- endoreg_db/utils/env.py +6 -2
- endoreg_db/utils/extract_specific_frames.py +24 -9
- endoreg_db/utils/file_operations.py +30 -18
- endoreg_db/utils/fix_video_path_direct.py +57 -41
- endoreg_db/utils/frame_anonymization_utils.py +157 -157
- endoreg_db/utils/hashs.py +3 -18
- endoreg_db/utils/links/requirement_link.py +96 -52
- endoreg_db/utils/ocr.py +30 -25
- endoreg_db/utils/operation_log.py +61 -0
- endoreg_db/utils/parse_and_generate_yaml.py +12 -13
- endoreg_db/utils/paths.py +6 -6
- endoreg_db/utils/permissions.py +40 -24
- endoreg_db/utils/pipelines/process_video_dir.py +50 -26
- endoreg_db/utils/product/sum_emissions.py +5 -3
- endoreg_db/utils/product/sum_weights.py +4 -2
- endoreg_db/utils/pydantic_models/__init__.py +3 -4
- endoreg_db/utils/requirement_operator_logic/_old/lab_value_operators.py +207 -107
- endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +252 -65
- endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +27 -10
- endoreg_db/utils/setup_config.py +21 -5
- endoreg_db/utils/storage.py +3 -1
- endoreg_db/utils/translation.py +19 -15
- endoreg_db/utils/uuid.py +1 -0
- endoreg_db/utils/validate_endo_roi.py +12 -4
- endoreg_db/utils/validate_subcategory_dict.py +26 -24
- endoreg_db/utils/validate_video_detailed.py +207 -149
- endoreg_db/utils/video/__init__.py +7 -3
- endoreg_db/utils/video/extract_frames.py +30 -18
- endoreg_db/utils/video/ffmpeg_wrapper.py +217 -52
- endoreg_db/utils/video/names.py +11 -6
- endoreg_db/utils/video/streaming_processor.py +175 -101
- endoreg_db/utils/video/video_splitter.py +30 -19
- endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +59 -50
- endoreg_db/views/__init__.py +0 -20
- endoreg_db/views/anonymization/__init__.py +6 -2
- endoreg_db/views/anonymization/media_management.py +2 -6
- endoreg_db/views/anonymization/overview.py +34 -1
- endoreg_db/views/anonymization/validate.py +79 -18
- endoreg_db/views/auth/__init__.py +1 -1
- endoreg_db/views/auth/keycloak.py +16 -14
- endoreg_db/views/examination/__init__.py +12 -15
- endoreg_db/views/examination/examination.py +5 -5
- endoreg_db/views/examination/examination_manifest_cache.py +5 -5
- endoreg_db/views/examination/get_finding_classification_choices.py +8 -5
- endoreg_db/views/examination/get_finding_classifications.py +9 -7
- endoreg_db/views/examination/get_findings.py +8 -10
- endoreg_db/views/examination/get_instruments.py +3 -2
- endoreg_db/views/examination/get_interventions.py +1 -1
- endoreg_db/views/finding/__init__.py +2 -2
- endoreg_db/views/finding/finding.py +58 -54
- endoreg_db/views/finding/get_classifications.py +1 -1
- endoreg_db/views/finding/get_interventions.py +1 -1
- endoreg_db/views/finding_classification/__init__.py +5 -5
- endoreg_db/views/finding_classification/finding_classification.py +5 -6
- endoreg_db/views/finding_classification/get_classification_choices.py +3 -4
- endoreg_db/views/media/__init__.py +13 -13
- endoreg_db/views/media/pdf_media.py +9 -9
- endoreg_db/views/media/sensitive_metadata.py +10 -7
- endoreg_db/views/media/video_media.py +4 -4
- endoreg_db/views/meta/__init__.py +1 -1
- endoreg_db/views/meta/sensitive_meta_list.py +20 -22
- endoreg_db/views/meta/sensitive_meta_verification.py +14 -11
- endoreg_db/views/misc/__init__.py +6 -34
- endoreg_db/views/misc/center.py +2 -1
- endoreg_db/views/misc/csrf.py +2 -1
- endoreg_db/views/misc/gender.py +2 -1
- endoreg_db/views/misc/stats.py +141 -106
- endoreg_db/views/patient/__init__.py +1 -3
- endoreg_db/views/patient/patient.py +141 -99
- endoreg_db/views/patient_examination/__init__.py +5 -5
- endoreg_db/views/patient_examination/patient_examination.py +43 -42
- endoreg_db/views/patient_examination/patient_examination_create.py +10 -15
- endoreg_db/views/patient_examination/patient_examination_detail.py +12 -15
- endoreg_db/views/patient_examination/patient_examination_list.py +21 -17
- endoreg_db/views/patient_examination/video.py +114 -80
- endoreg_db/views/patient_finding/__init__.py +1 -1
- endoreg_db/views/patient_finding/patient_finding.py +17 -10
- endoreg_db/views/patient_finding/patient_finding_optimized.py +127 -95
- endoreg_db/views/patient_finding_classification/__init__.py +1 -1
- endoreg_db/views/patient_finding_classification/pfc_create.py +35 -27
- endoreg_db/views/report/reimport.py +1 -1
- endoreg_db/views/report/report_stream.py +5 -8
- endoreg_db/views/requirement/__init__.py +2 -1
- endoreg_db/views/requirement/evaluate.py +7 -9
- endoreg_db/views/requirement/lookup.py +2 -3
- endoreg_db/views/requirement/lookup_store.py +0 -1
- endoreg_db/views/requirement/requirement_utils.py +2 -4
- endoreg_db/views/stats/__init__.py +4 -4
- endoreg_db/views/stats/stats_views.py +152 -115
- endoreg_db/views/video/__init__.py +18 -27
- endoreg_db/views/{ai → video/ai}/__init__.py +2 -2
- endoreg_db/views/{ai → video/ai}/label.py +20 -16
- endoreg_db/views/video/correction.py +5 -6
- endoreg_db/views/video/reimport.py +134 -99
- endoreg_db/views/video/segments_crud.py +134 -44
- endoreg_db/views/video/video_apply_mask.py +13 -12
- endoreg_db/views/video/video_correction.py +2 -1
- endoreg_db/views/video/video_download_processed.py +15 -15
- endoreg_db/views/video/video_meta_stats.py +7 -6
- endoreg_db/views/video/video_processing_history.py +3 -2
- endoreg_db/views/video/video_remove_frames.py +13 -12
- endoreg_db/views/video/video_stream.py +110 -82
- {endoreg_db-0.8.8.9.dist-info → endoreg_db-0.8.9.10.dist-info}/METADATA +9 -3
- {endoreg_db-0.8.8.9.dist-info → endoreg_db-0.8.9.10.dist-info}/RECORD +436 -433
- endoreg_db/import_files/processing/video_processing/video_cleanup_on_error.py +0 -119
- endoreg_db/management/commands/import_fallback_video.py +0 -203
- endoreg_db/management/commands/import_video.py +0 -422
- endoreg_db/management/commands/import_video_with_classification.py +0 -367
- endoreg_db/models/media/processing_history/processing_history.py +0 -96
- endoreg_db/serializers/label/__init__.py +0 -7
- endoreg_db/serializers/label_video_segment/_lvs_create.py +0 -149
- endoreg_db/serializers/label_video_segment/_lvs_update.py +0 -138
- endoreg_db/serializers/label_video_segment/_lvs_validate.py +0 -149
- endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +0 -99
- endoreg_db/serializers/label_video_segment/label_video_segment_update.py +0 -163
- endoreg_db/services/__old/pdf_import.py +0 -1487
- endoreg_db/services/__old/video_import.py +0 -1306
- endoreg_db/tasks/upload_tasks.py +0 -216
- endoreg_db/tasks/video_ingest.py +0 -161
- endoreg_db/tasks/video_processing_tasks.py +0 -327
- endoreg_db/views/misc/translation.py +0 -182
- {endoreg_db-0.8.8.9.dist-info → endoreg_db-0.8.9.10.dist-info}/WHEEL +0 -0
- {endoreg_db-0.8.8.9.dist-info → endoreg_db-0.8.9.10.dist-info}/licenses/LICENSE +0 -0
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import
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from pathlib import Path
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from endoreg_db.utils.uuid import get_uuid
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import hashlib
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from pathlib import Path
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def get_content_hash_filename(file: Path) -> tuple[str, str]:
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"""
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Returns a new filename with a uuid
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Returns a new filename with a uuid - This is the content hash -
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it is used to identify a raw video before processing when no other
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reliable info exists.
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It gets stored in processing_history model.
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uuid =
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uuid = sha256_file(file)
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def sha256_file(path: Path, chunk_size: int = 1024 * 1024) -> str:
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Compute a SHA-256 hash of the file contents in a streaming manner.
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Args:
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path: Path to the file on disk.
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chunk_size: Size of the chunks to read (default: 1MB).
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Returns:
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Hexadecimal SHA-256 digest (64 characters).
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break
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return h.hexdigest()
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return new_file, uuid
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def fix_video_paths_direct(db_path, storage_dir):
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"""Fix video file paths directly in SQLite database."""
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for pattern in ["**/*.mp4", "**/*.avi", "**/*.mov", "**/*.mkv"]:
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if
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if "_" in filename:
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uuid_part = filename.split("_")[0]
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uuid_part = filename.split(
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uuid_part = filename.split(".")[0]
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relative_path = file_path.relative_to(storage_dir)
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actual_files[uuid_part] = {
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"absolute_path": str(file_path),
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"relative_path": str(relative_path),
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"size_mb": file_path.stat().st_size / (1024 * 1024),
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}
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print(f"Found {len(actual_files)} video files")
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# Connect to database and check video records
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print("\n2. Checking database records...")
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try:
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conn = sqlite3.connect(db_path)
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cursor = conn.cursor()
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# Find video file table (might be different names)
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cursor.execute(
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cursor.execute(
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"SELECT name FROM sqlite_master WHERE type='table' AND name LIKE '%video%'"
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)
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tables = cursor.fetchall()
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print(f"Found video tables: {[t[0] for t in tables]}")
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# Check for VideoFile records
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video_table = None
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for table in [
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for table in ["endoreg_db_videofile", "videofile", "video_file"]:
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try:
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cursor.execute(f"SELECT COUNT(*) FROM {table}")
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count = cursor.fetchone()[0]
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@@ -65,24 +68,24 @@ def fix_video_paths_direct(db_path, storage_dir):
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break
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except sqlite3.OperationalError:
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continue
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print("❌ No video table found in database")
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return
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# Get video record 5
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cursor.execute(f"SELECT id, uuid, raw_file FROM {video_table} WHERE id = 5")
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print("❌ Video ID 5 not found in database")
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return
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video_id, uuid_str, current_raw_file = record
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print(
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print("\n3. Video ID 5 details:")
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print(f" UUID: {uuid_str}")
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print(f" Current raw_file: {current_raw_file}")
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# Check if current file exists
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if current_raw_file:
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current_full_path = storage_dir / current_raw_file
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@@ -90,30 +93,32 @@ def fix_video_paths_direct(db_path, storage_dir):
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print(f" File exists: {file_exists}")
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if not file_exists:
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print(f" Full path checked: {current_full_path}")
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# Find matching file
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98
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if uuid_str in actual_files:
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file_info = actual_files[uuid_str]
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print(
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print("\n4. Found matching file:")
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101
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print(f" Path: {file_info['absolute_path']}")
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print(f" Size: {file_info['size_mb']:.1f} MB")
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print(f" Relative path: {file_info['relative_path']}")
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if current_raw_file != file_info[
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print(
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if current_raw_file != file_info["relative_path"]:
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print("\n5. 🔧 FIXING PATH:")
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107
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print(f" FROM: {current_raw_file}")
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print(f" TO: {file_info['relative_path']}")
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-
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# Update the database with transaction safety
|
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try:
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cursor.execute(
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-
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cursor.execute(
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f"UPDATE {video_table} SET raw_file = ? WHERE id = ?",
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(file_info["relative_path"], video_id),
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)
|
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116
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conn.commit()
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117
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print("✅ Database updated successfully!")
|
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118
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except Exception as e:
|
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119
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conn.rollback()
|
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print(f"❌ Failed to update database: {e}")
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print("\n6. 🎯 NEXT STEPS:")
|
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print(" 1. Restart your Django development server")
|
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124
|
print(" 2. Test video streaming in the frontend")
|
|
@@ -125,17 +130,28 @@ def fix_video_paths_direct(db_path, storage_dir):
|
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125
130
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print("Available UUIDs in storage:")
|
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126
131
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for uuid_key in list(actual_files.keys())[:5]:
|
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132
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print(f" - {uuid_key}")
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-
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conn.close()
|
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|
-
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136
|
except Exception as e:
|
|
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137
|
print(f"❌ Database error: {e}")
|
|
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138
|
|
|
139
|
+
|
|
134
140
|
if __name__ == "__main__":
|
|
135
|
-
parser = argparse.ArgumentParser(
|
|
136
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-
|
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137
|
-
|
|
138
|
-
parser.add_argument(
|
|
139
|
-
|
|
141
|
+
parser = argparse.ArgumentParser(
|
|
142
|
+
description="Direct fix for video file path issues in SQLite DB."
|
|
143
|
+
)
|
|
144
|
+
parser.add_argument(
|
|
145
|
+
"--db-path",
|
|
146
|
+
type=str,
|
|
147
|
+
default=os.environ.get("ENDOREG_DB_PATH", "./db.sqlite3"),
|
|
148
|
+
help="Path to the SQLite database file (default: ./db.sqlite3 or $ENDOREG_DB_PATH)",
|
|
149
|
+
)
|
|
150
|
+
parser.add_argument(
|
|
151
|
+
"--storage-dir",
|
|
152
|
+
type=str,
|
|
153
|
+
default=os.environ.get("ENDOREG_STORAGE_DIR", "./storage"),
|
|
154
|
+
help="Path to the storage directory (default: ./storage or $ENDOREG_STORAGE_DIR)",
|
|
155
|
+
)
|
|
140
156
|
args = parser.parse_args()
|
|
141
|
-
fix_video_paths_direct(args.db_path, args.storage_dir)
|
|
157
|
+
fix_video_paths_direct(args.db_path, args.storage_dir)
|