endoreg-db 0.8.4.4__py3-none-any.whl → 0.8.8.0__py3-none-any.whl
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- endoreg_db/authz/auth.py +74 -0
- endoreg_db/authz/backends.py +168 -0
- endoreg_db/authz/management/commands/list_routes.py +18 -0
- endoreg_db/authz/middleware.py +83 -0
- endoreg_db/authz/permissions.py +127 -0
- endoreg_db/authz/policy.py +218 -0
- endoreg_db/authz/views_auth.py +66 -0
- endoreg_db/config/env.py +13 -8
- endoreg_db/data/__init__.py +8 -31
- endoreg_db/data/_examples/disease.yaml +55 -0
- endoreg_db/data/_examples/disease_classification.yaml +13 -0
- endoreg_db/data/_examples/disease_classification_choice.yaml +62 -0
- endoreg_db/data/_examples/event.yaml +64 -0
- endoreg_db/data/_examples/examination.yaml +72 -0
- endoreg_db/data/_examples/finding/anatomy_colon.yaml +128 -0
- endoreg_db/data/_examples/finding/colonoscopy.yaml +40 -0
- endoreg_db/data/_examples/finding/colonoscopy_bowel_prep.yaml +56 -0
- endoreg_db/data/_examples/finding/complication.yaml +16 -0
- endoreg_db/data/_examples/finding/data.yaml +105 -0
- endoreg_db/data/_examples/finding/examination_setting.yaml +16 -0
- endoreg_db/data/_examples/finding/medication_related.yaml +18 -0
- endoreg_db/data/_examples/finding/outcome.yaml +12 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_bowel_preparation.yaml +68 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_jnet.yaml +22 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_kudo.yaml +25 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_size.yaml +68 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_location.yaml +80 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_lst.yaml +21 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_nice.yaml +20 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_paris.yaml +26 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_sano.yaml +22 -0
- endoreg_db/data/_examples/finding_classification/colonoscopy_summary.yaml +53 -0
- endoreg_db/data/_examples/finding_classification/complication_generic.yaml +25 -0
- endoreg_db/data/_examples/finding_classification/examination_setting_generic.yaml +40 -0
- endoreg_db/data/_examples/finding_classification/histology_colo.yaml +51 -0
- endoreg_db/data/_examples/finding_classification/intervention_required.yaml +26 -0
- endoreg_db/data/_examples/finding_classification/medication_related.yaml +23 -0
- endoreg_db/data/_examples/finding_classification/visualized.yaml +33 -0
- endoreg_db/data/_examples/finding_classification_choice/bowel_preparation.yaml +78 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_lst.yaml +15 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_nice.yaml +17 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_paris.yaml +57 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_sano.yaml +14 -0
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
- endoreg_db/data/_examples/finding_classification_choice/colonoscopy_location.yaml +229 -0
- endoreg_db/data/_examples/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
- endoreg_db/data/_examples/finding_classification_choice/colonoscopy_size.yaml +82 -0
- endoreg_db/data/_examples/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
- endoreg_db/data/_examples/finding_classification_choice/complication_generic_types.yaml +15 -0
- endoreg_db/data/_examples/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
- endoreg_db/data/_examples/finding_classification_choice/histology.yaml +24 -0
- endoreg_db/data/_examples/finding_classification_choice/histology_polyp.yaml +20 -0
- endoreg_db/data/_examples/finding_classification_choice/outcome.yaml +19 -0
- endoreg_db/data/_examples/finding_classification_choice/yes_no_na.yaml +11 -0
- endoreg_db/data/_examples/finding_classification_type/colonoscopy_basic.yaml +48 -0
- endoreg_db/data/_examples/finding_intervention/endoscopy.yaml +43 -0
- endoreg_db/data/_examples/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
- endoreg_db/data/_examples/finding_intervention/endoscopy_egd.yaml +128 -0
- endoreg_db/data/_examples/finding_intervention/endoscopy_ercp.yaml +32 -0
- endoreg_db/data/_examples/finding_intervention/endoscopy_eus_lower.yaml +9 -0
- endoreg_db/data/_examples/finding_intervention/endoscopy_eus_upper.yaml +36 -0
- endoreg_db/data/_examples/finding_intervention_type/endoscopy.yaml +15 -0
- endoreg_db/data/_examples/finding_type/data.yaml +43 -0
- endoreg_db/data/_examples/requirement/age.yaml +26 -0
- endoreg_db/data/_examples/requirement/colonoscopy_baseline_austria.yaml +45 -0
- endoreg_db/data/_examples/requirement/disease_cardiovascular.yaml +79 -0
- endoreg_db/data/_examples/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
- endoreg_db/data/_examples/requirement/disease_hepatology.yaml +12 -0
- endoreg_db/data/_examples/requirement/disease_misc.yaml +12 -0
- endoreg_db/data/_examples/requirement/disease_renal.yaml +96 -0
- endoreg_db/data/_examples/requirement/endoscopy_bleeding_risk.yaml +59 -0
- endoreg_db/data/_examples/requirement/event_cardiology.yaml +251 -0
- endoreg_db/data/_examples/requirement/event_requirements.yaml +145 -0
- endoreg_db/data/_examples/requirement/finding_colon_polyp.yaml +50 -0
- endoreg_db/data/_examples/requirement/gender.yaml +25 -0
- endoreg_db/data/_examples/requirement/lab_value.yaml +441 -0
- endoreg_db/data/_examples/requirement/medication.yaml +93 -0
- endoreg_db/data/_examples/requirement_operator/age.yaml +13 -0
- endoreg_db/data/_examples/requirement_operator/lab_operators.yaml +129 -0
- endoreg_db/data/_examples/requirement_operator/model_operators.yaml +96 -0
- endoreg_db/data/_examples/requirement_set/01_endoscopy_generic.yaml +48 -0
- endoreg_db/data/_examples/requirement_set/colonoscopy_austria_screening.yaml +57 -0
- endoreg_db/data/_examples/yaml_examples.xlsx +0 -0
- endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +4 -3
- endoreg_db/data/event_classification/data.yaml +4 -0
- endoreg_db/data/event_classification_choice/data.yaml +9 -0
- endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +43 -70
- endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +22 -52
- endoreg_db/data/finding_classification/colonoscopy_location.yaml +31 -62
- endoreg_db/data/finding_classification/histology_colo.yaml +28 -36
- endoreg_db/data/requirement/colon_polyp_intervention.yaml +49 -0
- endoreg_db/data/requirement/coloreg_colon_polyp.yaml +49 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +31 -12
- endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
- endoreg_db/data/requirement_set/02_endoscopy_bleeding_risk.yaml +46 -0
- endoreg_db/data/requirement_set/90_coloreg.yaml +178 -0
- endoreg_db/data/requirement_set/_old_ +109 -0
- endoreg_db/data/requirement_set_type/data.yaml +21 -0
- endoreg_db/data/setup_config.yaml +4 -4
- endoreg_db/data/tag/requirement_set_tags.yaml +21 -0
- endoreg_db/exceptions.py +5 -2
- endoreg_db/helpers/data_loader.py +1 -1
- endoreg_db/management/commands/create_model_meta_from_huggingface.py +21 -10
- endoreg_db/management/commands/create_multilabel_model_meta.py +299 -129
- endoreg_db/management/commands/import_video.py +9 -10
- endoreg_db/management/commands/import_video_with_classification.py +1 -1
- endoreg_db/management/commands/init_default_ai_model.py +1 -1
- endoreg_db/management/commands/list_routes.py +18 -0
- endoreg_db/management/commands/load_ai_model_data.py +2 -1
- endoreg_db/management/commands/load_center_data.py +12 -12
- endoreg_db/management/commands/load_requirement_data.py +60 -31
- endoreg_db/management/commands/load_requirement_set_tags.py +95 -0
- endoreg_db/management/commands/setup_endoreg_db.py +14 -10
- endoreg_db/management/commands/storage_management.py +271 -203
- endoreg_db/migrations/0001_initial.py +1799 -1300
- endoreg_db/migrations/0002_requirementset_depends_on.py +18 -0
- endoreg_db/migrations/_old/0001_initial.py +1857 -0
- endoreg_db/migrations/_old/0004_employee_city_employee_post_code_employee_street_and_more.py +68 -0
- endoreg_db/migrations/_old/0004_remove_casetemplate_rules_and_more.py +77 -0
- endoreg_db/migrations/_old/0005_merge_20251111_1003.py +14 -0
- endoreg_db/migrations/_old/0006_sensitivemeta_anonymized_text_and_more.py +68 -0
- endoreg_db/migrations/_old/0007_remove_rule_attribute_dtype_remove_rule_rule_type_and_more.py +89 -0
- endoreg_db/migrations/_old/0008_remove_event_event_classification_and_more.py +27 -0
- endoreg_db/migrations/_old/0009_alter_modelmeta_options_and_more.py +21 -0
- endoreg_db/models/__init__.py +78 -123
- endoreg_db/models/administration/__init__.py +21 -42
- endoreg_db/models/administration/ai/active_model.py +2 -2
- endoreg_db/models/administration/ai/ai_model.py +7 -6
- endoreg_db/models/administration/case/__init__.py +1 -15
- endoreg_db/models/administration/case/case.py +3 -3
- endoreg_db/models/administration/case/case_template/__init__.py +2 -14
- endoreg_db/models/administration/case/case_template/case_template.py +2 -124
- endoreg_db/models/administration/case/case_template/case_template_rule.py +2 -268
- endoreg_db/models/administration/case/case_template/case_template_rule_value.py +2 -85
- endoreg_db/models/administration/case/case_template/case_template_type.py +2 -25
- endoreg_db/models/administration/center/center.py +33 -19
- endoreg_db/models/administration/center/center_product.py +12 -9
- endoreg_db/models/administration/center/center_resource.py +25 -19
- endoreg_db/models/administration/center/center_shift.py +21 -17
- endoreg_db/models/administration/center/center_waste.py +16 -8
- endoreg_db/models/administration/person/__init__.py +2 -0
- endoreg_db/models/administration/person/employee/employee.py +10 -5
- endoreg_db/models/administration/person/employee/employee_qualification.py +9 -4
- endoreg_db/models/administration/person/employee/employee_type.py +12 -6
- endoreg_db/models/administration/person/examiner/examiner.py +13 -11
- endoreg_db/models/administration/person/patient/__init__.py +2 -0
- endoreg_db/models/administration/person/patient/patient.py +103 -100
- endoreg_db/models/administration/person/patient/patient_external_id.py +37 -0
- endoreg_db/models/administration/person/person.py +4 -0
- endoreg_db/models/administration/person/profession/__init__.py +8 -4
- endoreg_db/models/administration/person/user/portal_user_information.py +11 -7
- endoreg_db/models/administration/product/product.py +20 -15
- endoreg_db/models/administration/product/product_material.py +17 -18
- endoreg_db/models/administration/product/product_weight.py +12 -8
- endoreg_db/models/administration/product/reference_product.py +23 -55
- endoreg_db/models/administration/qualification/qualification.py +7 -3
- endoreg_db/models/administration/qualification/qualification_type.py +7 -3
- endoreg_db/models/administration/shift/scheduled_days.py +8 -5
- endoreg_db/models/administration/shift/shift.py +16 -12
- endoreg_db/models/administration/shift/shift_type.py +23 -31
- endoreg_db/models/label/__init__.py +7 -8
- endoreg_db/models/label/annotation/image_classification.py +10 -9
- endoreg_db/models/label/annotation/video_segmentation_annotation.py +8 -5
- endoreg_db/models/label/label.py +15 -15
- endoreg_db/models/label/label_set.py +19 -6
- endoreg_db/models/label/label_type.py +1 -1
- endoreg_db/models/label/label_video_segment/_create_from_video.py +5 -8
- endoreg_db/models/label/label_video_segment/label_video_segment.py +76 -102
- endoreg_db/models/label/video_segmentation_label.py +4 -0
- endoreg_db/models/label/video_segmentation_labelset.py +4 -3
- endoreg_db/models/media/frame/frame.py +22 -22
- endoreg_db/models/media/pdf/raw_pdf.py +249 -177
- endoreg_db/models/media/pdf/report_file.py +25 -29
- endoreg_db/models/media/pdf/report_reader/report_reader_config.py +30 -46
- endoreg_db/models/media/pdf/report_reader/report_reader_flag.py +23 -7
- endoreg_db/models/media/video/__init__.py +1 -0
- endoreg_db/models/media/video/create_from_file.py +48 -56
- endoreg_db/models/media/video/pipe_1.py +30 -33
- endoreg_db/models/media/video/pipe_2.py +8 -9
- endoreg_db/models/media/video/video_file.py +359 -204
- endoreg_db/models/media/video/video_file_ai.py +288 -74
- endoreg_db/models/media/video/video_file_anonymize.py +38 -38
- endoreg_db/models/media/video/video_file_frames/__init__.py +3 -1
- endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +6 -8
- endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +7 -9
- endoreg_db/models/media/video/video_file_frames/_delete_frames.py +9 -8
- endoreg_db/models/media/video/video_file_frames/_extract_frames.py +38 -45
- endoreg_db/models/media/video/video_file_frames/_get_frame.py +6 -8
- endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +4 -18
- endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +4 -3
- endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +7 -6
- endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +6 -8
- endoreg_db/models/media/video/video_file_frames/_get_frames.py +6 -8
- endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +15 -25
- endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +26 -23
- endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +23 -14
- endoreg_db/models/media/video/video_file_io.py +109 -62
- endoreg_db/models/media/video/video_file_meta/get_crop_template.py +3 -3
- endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +5 -3
- endoreg_db/models/media/video/video_file_meta/get_fps.py +37 -34
- endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +19 -25
- endoreg_db/models/media/video/video_file_meta/text_meta.py +41 -38
- endoreg_db/models/media/video/video_file_meta/video_meta.py +14 -7
- endoreg_db/models/media/video/video_file_segments.py +24 -17
- endoreg_db/models/media/video/video_metadata.py +19 -35
- endoreg_db/models/media/video/video_processing.py +96 -95
- endoreg_db/models/medical/contraindication/__init__.py +13 -3
- endoreg_db/models/medical/disease.py +22 -16
- endoreg_db/models/medical/event.py +31 -18
- endoreg_db/models/medical/examination/__init__.py +13 -6
- endoreg_db/models/medical/examination/examination.py +17 -18
- endoreg_db/models/medical/examination/examination_indication.py +26 -25
- endoreg_db/models/medical/examination/examination_time.py +16 -6
- endoreg_db/models/medical/examination/examination_time_type.py +9 -6
- endoreg_db/models/medical/examination/examination_type.py +3 -4
- endoreg_db/models/medical/finding/finding.py +38 -39
- endoreg_db/models/medical/finding/finding_classification.py +37 -48
- endoreg_db/models/medical/finding/finding_intervention.py +27 -22
- endoreg_db/models/medical/finding/finding_type.py +13 -12
- endoreg_db/models/medical/hardware/endoscope.py +20 -26
- endoreg_db/models/medical/hardware/endoscopy_processor.py +2 -2
- endoreg_db/models/medical/laboratory/lab_value.py +62 -91
- endoreg_db/models/medical/medication/medication.py +22 -10
- endoreg_db/models/medical/medication/medication_indication.py +29 -3
- endoreg_db/models/medical/medication/medication_indication_type.py +25 -14
- endoreg_db/models/medical/medication/medication_intake_time.py +31 -19
- endoreg_db/models/medical/medication/medication_schedule.py +27 -16
- endoreg_db/models/medical/organ/__init__.py +15 -12
- endoreg_db/models/medical/patient/medication_examples.py +1 -5
- endoreg_db/models/medical/patient/patient_disease.py +20 -23
- endoreg_db/models/medical/patient/patient_event.py +19 -22
- endoreg_db/models/medical/patient/patient_examination.py +48 -54
- endoreg_db/models/medical/patient/patient_examination_indication.py +16 -14
- endoreg_db/models/medical/patient/patient_finding.py +122 -139
- endoreg_db/models/medical/patient/patient_finding_classification.py +44 -49
- endoreg_db/models/medical/patient/patient_finding_intervention.py +8 -19
- endoreg_db/models/medical/patient/patient_lab_sample.py +28 -23
- endoreg_db/models/medical/patient/patient_lab_value.py +82 -89
- endoreg_db/models/medical/patient/patient_medication.py +27 -38
- endoreg_db/models/medical/patient/patient_medication_schedule.py +28 -36
- endoreg_db/models/medical/risk/risk.py +7 -6
- endoreg_db/models/medical/risk/risk_type.py +8 -5
- endoreg_db/models/metadata/model_meta.py +60 -29
- endoreg_db/models/metadata/model_meta_logic.py +139 -18
- endoreg_db/models/metadata/pdf_meta.py +19 -24
- endoreg_db/models/metadata/sensitive_meta.py +102 -85
- endoreg_db/models/metadata/sensitive_meta_logic.py +383 -43
- endoreg_db/models/metadata/video_meta.py +51 -31
- endoreg_db/models/metadata/video_prediction_logic.py +16 -23
- endoreg_db/models/metadata/video_prediction_meta.py +29 -33
- endoreg_db/models/other/distribution/date_value_distribution.py +89 -29
- endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +21 -5
- endoreg_db/models/other/distribution/numeric_value_distribution.py +114 -53
- endoreg_db/models/other/distribution/single_categorical_value_distribution.py +4 -3
- endoreg_db/models/other/emission/emission_factor.py +18 -8
- endoreg_db/models/other/gender.py +10 -5
- endoreg_db/models/other/information_source.py +25 -25
- endoreg_db/models/other/material.py +9 -5
- endoreg_db/models/other/resource.py +6 -4
- endoreg_db/models/other/tag.py +10 -5
- endoreg_db/models/other/transport_route.py +13 -8
- endoreg_db/models/other/unit.py +10 -6
- endoreg_db/models/other/waste.py +6 -5
- endoreg_db/models/requirement/requirement.py +580 -272
- endoreg_db/models/requirement/requirement_error.py +85 -0
- endoreg_db/models/requirement/requirement_evaluation/evaluate_with_dependencies.py +268 -0
- endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +3 -6
- endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +90 -64
- endoreg_db/models/requirement/requirement_operator.py +36 -33
- endoreg_db/models/requirement/requirement_set.py +74 -57
- endoreg_db/models/state/__init__.py +4 -4
- endoreg_db/models/state/abstract.py +2 -2
- endoreg_db/models/state/anonymization.py +12 -0
- endoreg_db/models/state/audit_ledger.py +46 -47
- endoreg_db/models/state/label_video_segment.py +9 -0
- endoreg_db/models/state/raw_pdf.py +40 -46
- endoreg_db/models/state/sensitive_meta.py +6 -2
- endoreg_db/models/state/video.py +58 -53
- endoreg_db/models/upload_job.py +32 -55
- endoreg_db/models/utils.py +1 -2
- endoreg_db/root_urls.py +21 -2
- endoreg_db/serializers/__init__.py +26 -57
- endoreg_db/serializers/anonymization.py +18 -10
- endoreg_db/serializers/meta/report_meta.py +1 -1
- endoreg_db/serializers/meta/sensitive_meta_detail.py +63 -118
- endoreg_db/serializers/misc/__init__.py +1 -1
- endoreg_db/serializers/misc/file_overview.py +33 -91
- endoreg_db/serializers/misc/{vop_patient_data.py → sensitive_patient_data.py} +1 -1
- endoreg_db/serializers/requirements/requirement_sets.py +92 -22
- endoreg_db/serializers/video/segmentation.py +2 -1
- endoreg_db/serializers/video/video_processing_history.py +20 -5
- endoreg_db/serializers/video_examination.py +198 -0
- endoreg_db/services/anonymization.py +75 -73
- endoreg_db/services/lookup_service.py +256 -73
- endoreg_db/services/lookup_store.py +174 -30
- endoreg_db/services/pdf_import.py +711 -310
- endoreg_db/services/storage_aware_video_processor.py +140 -114
- endoreg_db/services/video_import.py +266 -117
- endoreg_db/urls/__init__.py +27 -27
- endoreg_db/urls/label_video_segments.py +2 -0
- endoreg_db/urls/media.py +108 -66
- endoreg_db/urls/root_urls.py +29 -0
- endoreg_db/utils/__init__.py +15 -5
- endoreg_db/utils/ai/multilabel_classification_net.py +116 -20
- endoreg_db/utils/case_generator/__init__.py +3 -0
- endoreg_db/utils/dataloader.py +88 -16
- endoreg_db/utils/defaults/set_default_center.py +32 -0
- endoreg_db/utils/names.py +22 -16
- endoreg_db/utils/permissions.py +2 -1
- endoreg_db/utils/pipelines/process_video_dir.py +1 -1
- endoreg_db/utils/requirement_operator_logic/model_evaluators.py +414 -127
- endoreg_db/utils/setup_config.py +8 -5
- endoreg_db/utils/storage.py +115 -0
- endoreg_db/utils/validate_endo_roi.py +8 -2
- endoreg_db/utils/video/ffmpeg_wrapper.py +184 -188
- endoreg_db/views/__init__.py +5 -12
- endoreg_db/views/anonymization/media_management.py +198 -163
- endoreg_db/views/anonymization/overview.py +4 -1
- endoreg_db/views/anonymization/validate.py +174 -40
- endoreg_db/views/media/__init__.py +2 -0
- endoreg_db/views/media/pdf_media.py +131 -150
- endoreg_db/views/media/sensitive_metadata.py +46 -6
- endoreg_db/views/media/video_media.py +89 -82
- endoreg_db/views/media/video_segments.py +187 -260
- endoreg_db/views/meta/sensitive_meta_detail.py +0 -63
- endoreg_db/views/patient/patient.py +5 -4
- endoreg_db/views/pdf/__init__.py +5 -8
- endoreg_db/views/pdf/pdf_stream.py +186 -0
- endoreg_db/views/pdf/pdf_stream_views.py +0 -127
- endoreg_db/views/pdf/reimport.py +86 -91
- endoreg_db/views/requirement/evaluate.py +188 -187
- endoreg_db/views/requirement/lookup.py +186 -288
- endoreg_db/views/requirement/requirement_utils.py +89 -0
- endoreg_db/views/video/__init__.py +0 -4
- endoreg_db/views/video/correction.py +2 -2
- endoreg_db/views/video/video_examination_viewset.py +202 -289
- {endoreg_db-0.8.4.4.dist-info → endoreg_db-0.8.8.0.dist-info}/METADATA +7 -3
- {endoreg_db-0.8.4.4.dist-info → endoreg_db-0.8.8.0.dist-info}/RECORD +350 -255
- endoreg_db/models/administration/permissions/__init__.py +0 -44
- endoreg_db/models/media/video/refactor_plan.md +0 -0
- endoreg_db/models/media/video/video_file_frames.py +0 -0
- endoreg_db/models/metadata/frame_ocr_result.py +0 -0
- endoreg_db/models/rule/__init__.py +0 -13
- endoreg_db/models/rule/rule.py +0 -27
- endoreg_db/models/rule/rule_applicator.py +0 -224
- endoreg_db/models/rule/rule_attribute_dtype.py +0 -17
- endoreg_db/models/rule/rule_type.py +0 -20
- endoreg_db/models/rule/ruleset.py +0 -17
- endoreg_db/serializers/video/video_metadata.py +0 -105
- endoreg_db/urls/report.py +0 -48
- endoreg_db/urls/video.py +0 -61
- endoreg_db/utils/case_generator/case_generator.py +0 -159
- endoreg_db/utils/case_generator/utils.py +0 -30
- endoreg_db/views/pdf/pdf_media.py +0 -239
- endoreg_db/views/report/__init__.py +0 -9
- endoreg_db/views/report/report_list.py +0 -112
- endoreg_db/views/report/report_with_secure_url.py +0 -28
- endoreg_db/views/report/start_examination.py +0 -7
- endoreg_db/views/video/video_media.py +0 -158
- endoreg_db/views.py +0 -0
- /endoreg_db/data/{requirement_set → _examples/requirement_set}/endoscopy_bleeding_risk.yaml +0 -0
- /endoreg_db/migrations/{0002_add_video_correction_models.py → _old/0002_add_video_correction_models.py} +0 -0
- /endoreg_db/migrations/{0003_add_center_display_name.py → _old/0003_add_center_display_name.py} +0 -0
- {endoreg_db-0.8.4.4.dist-info → endoreg_db-0.8.8.0.dist-info}/WHEEL +0 -0
- {endoreg_db-0.8.4.4.dist-info → endoreg_db-0.8.8.0.dist-info}/licenses/LICENSE +0 -0
endoreg_db/views/pdf/reimport.py
CHANGED
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@@ -1,19 +1,22 @@
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1
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-
from rest_framework.views import APIView
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-
from rest_framework.response import Response
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from rest_framework import status
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import logging
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-
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from django.db import transaction
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from rest_framework import status
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from rest_framework.response import Response
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from rest_framework.views import APIView
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from ...models import RawPdfFile, SensitiveMeta
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from ...services.pdf_import import PdfImportService
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logger = logging.getLogger(__name__)
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class PdfReimportView(APIView):
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"""
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API endpoint to re-import a pdf file and regenerate metadata.
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This is useful when OCR failed or metadata is incomplete.
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"""
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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self.pdf_service = PdfImportService()
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@@ -22,140 +25,132 @@ class PdfReimportView(APIView):
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"""
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Re-import a pdf file to regenerate SensitiveMeta and other metadata.
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Instead of creating a new pdf, this updates the existing one.
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-
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Args:
|
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request: HTTP request object
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pk: PDF primary key (ID)
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"""
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pdf_id = pk # Align with media framework naming convention
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-
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# Validate pdf_id parameter
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if not pdf_id or not isinstance(pdf_id, int):
|
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return Response(
|
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{"error": "Invalid PDF ID provided."},
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status=status.HTTP_400_BAD_REQUEST
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{"error": "Invalid PDF ID provided."},
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status=status.HTTP_400_BAD_REQUEST,
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)
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try:
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pdf = RawPdfFile.objects.get(id=pdf_id)
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logger.info(f"Found PDF {pdf.
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logger.info(f"Found PDF {pdf.pdf_hash} (ID: {pdf_id}) for re-import")
|
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45
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except RawPdfFile.DoesNotExist:
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logger.warning(f"PDF with ID {pdf_id} not found")
|
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return Response(
|
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{"error": f"PDF with ID {pdf_id} not found."},
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status=status.HTTP_404_NOT_FOUND
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{"error": f"PDF with ID {pdf_id} not found."},
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status=status.HTTP_404_NOT_FOUND,
|
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)
|
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# Get raw file path using the model method
|
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raw_file_path = pdf.get_raw_file_path()
|
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raw_file_path = Path(pdf.file.path)
|
|
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if not raw_file_path.exists():
|
|
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-
logger.error(f"Raw file not found on disk: {raw_file_path}")
|
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55
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+
if not raw_file_path or not raw_file_path.exists():
|
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+
logger.error(f"Raw PDF file not found for hash {pdf.pdf_hash}: {raw_file_path}")
|
|
55
57
|
return Response(
|
|
56
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{"error": f"PDF file not found
|
|
57
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-
status=status.
|
|
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+
{"error": f"Raw PDF file not found for PDF {pdf.pdf_hash}. Please upload the original file again."},
|
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status=status.HTTP_404_NOT_FOUND,
|
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60
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)
|
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# Check if PDF has required relationships
|
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63
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if not pdf.center:
|
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-
logger.warning(f"PDF {pdf.
|
|
64
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+
logger.warning(f"PDF {pdf.pdf_hash} has no associated center")
|
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return Response(
|
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{"error": "
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-
status=status.HTTP_400_BAD_REQUEST
|
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{"error": "PDF has no associated center."},
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status=status.HTTP_400_BAD_REQUEST,
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)
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try:
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logger.info(f"Starting
|
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logger.info(f"Starting re-import for PDF {pdf.pdf_hash} (ID: {pdf_id})")
|
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|
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with transaction.atomic():
|
|
72
74
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# Clear existing metadata to force regeneration
|
|
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old_meta_id = None
|
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if pdf.sensitive_meta:
|
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-
old_meta_id = pdf.sensitive_meta.
|
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76
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-
logger.info(f"Clearing existing SensitiveMeta {old_meta_id} for
|
|
77
|
+
old_meta_id = pdf.sensitive_meta.pk
|
|
78
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+
logger.info(f"Clearing existing SensitiveMeta {old_meta_id} for PDF {pdf.pdf_hash}")
|
|
77
79
|
pdf.sensitive_meta = None
|
|
78
|
-
pdf.save(update_fields=[
|
|
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-
|
|
80
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+
pdf.save(update_fields=["sensitive_meta"])
|
|
81
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|
|
80
82
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# Delete the old SensitiveMeta record
|
|
81
83
|
try:
|
|
82
|
-
SensitiveMeta.objects.filter(
|
|
84
|
+
SensitiveMeta.objects.filter(pk=old_meta_id).delete()
|
|
83
85
|
logger.info(f"Deleted old SensitiveMeta {old_meta_id}")
|
|
84
86
|
except Exception as e:
|
|
85
87
|
logger.warning(f"Could not delete old SensitiveMeta {old_meta_id}: {e}")
|
|
86
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-
|
|
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88
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-
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89
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-
|
|
91
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# Ensure minimum patient data is available
|
|
92
|
-
logger.info(f"Ensuring minimum patient data for {pdf.uuid}")
|
|
93
|
-
self.pdf_service._ensure_default_patient_data(pdf)
|
|
94
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-
|
|
95
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-
# Refresh from database to get updated data
|
|
96
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-
pdf.refresh_from_db()
|
|
97
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-
|
|
98
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-
# Use VideoImportService for anonymization
|
|
88
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+
|
|
89
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# Use PdfImportService for reprocessing
|
|
99
90
|
try:
|
|
100
|
-
|
|
101
|
-
logger.info(f"Starting anonymization using VideoImportService for {pdf.uuid}")
|
|
91
|
+
logger.info(f"Starting reprocessing using PdfImportService for {pdf.pdf_hash}")
|
|
102
92
|
self.pdf_service.import_and_anonymize(
|
|
103
93
|
file_path=raw_file_path,
|
|
104
94
|
center_name=pdf.center.name,
|
|
105
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-
|
|
106
|
-
|
|
107
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-
delete_source=False
|
|
95
|
+
delete_source=False, # Don't delete during reimport
|
|
96
|
+
retry=True, # Mark as retry attempt
|
|
108
97
|
)
|
|
109
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-
|
|
110
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logger.info(f"
|
|
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-
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123
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|
|
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+
logger.info(f"PdfImportService reprocessing completed for {pdf.pdf_hash}")
|
|
100
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|
|
101
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+
# Refresh to get updated state
|
|
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+
pdf.refresh_from_db()
|
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+
|
|
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+
return Response(
|
|
105
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+
{
|
|
106
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+
"message": "PDF re-import completed successfully.",
|
|
107
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+
"pdf_id": pdf_id,
|
|
108
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+
"pdf_hash": str(pdf.pdf_hash),
|
|
109
|
+
"sensitive_meta_created": pdf.sensitive_meta is not None,
|
|
110
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+
"sensitive_meta_id": pdf.sensitive_meta.pk if pdf.sensitive_meta else None,
|
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111
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+
"text_extracted": bool(pdf.text),
|
|
112
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+
"anonymized": pdf.anonymized,
|
|
113
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+
"status": "done",
|
|
114
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+
},
|
|
115
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+
status=status.HTTP_200_OK,
|
|
116
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+
)
|
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117
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+
|
|
124
118
|
except Exception as e:
|
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logger.exception(f"
|
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"sensitive_meta_created": pdf.sensitive_meta is not None,
|
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|
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"sensitive_meta_id": pdf.sensitive_meta.id if pdf.sensitive_meta else None,
|
|
137
|
-
"updated_in_place": True,
|
|
138
|
-
"status": "done"
|
|
139
|
-
}, status=status.HTTP_200_OK)
|
|
119
|
+
logger.exception(f"PdfImportService reprocessing failed for PDF {pdf.pdf_hash}: {e}")
|
|
120
|
+
return Response(
|
|
121
|
+
{
|
|
122
|
+
"error": f"Reprocessing failed: {str(e)}",
|
|
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|
+
"error_type": "processing_error",
|
|
124
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+
"pdf_id": pdf_id,
|
|
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+
"pdf_hash": str(pdf.pdf_hash),
|
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+
},
|
|
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+
status=status.HTTP_500_INTERNAL_SERVER_ERROR,
|
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+
)
|
|
140
129
|
|
|
141
130
|
except Exception as e:
|
|
142
|
-
logger.error(f"Failed to re-import
|
|
143
|
-
|
|
131
|
+
logger.error(f"Failed to re-import PDF {pdf.pdf_hash}: {str(e)}", exc_info=True)
|
|
132
|
+
|
|
144
133
|
# Handle specific error types
|
|
145
134
|
error_msg = str(e)
|
|
146
135
|
if any(phrase in error_msg.lower() for phrase in ["insufficient storage", "no space left", "disk full"]):
|
|
147
136
|
# Storage error - return specific error message
|
|
148
|
-
return Response(
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
|
|
137
|
+
return Response(
|
|
138
|
+
{
|
|
139
|
+
"error": f"Storage error during re-import: {error_msg}",
|
|
140
|
+
"error_type": "storage_error",
|
|
141
|
+
"pdf_id": pdf_id,
|
|
142
|
+
"pdf_hash": str(pdf.pdf_hash),
|
|
143
|
+
},
|
|
144
|
+
status=status.HTTP_507_INSUFFICIENT_STORAGE,
|
|
145
|
+
)
|
|
154
146
|
else:
|
|
155
147
|
# Other errors
|
|
156
|
-
return Response(
|
|
157
|
-
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
|
|
148
|
+
return Response(
|
|
149
|
+
{
|
|
150
|
+
"error": f"Re-import failed: {error_msg}",
|
|
151
|
+
"error_type": "processing_error",
|
|
152
|
+
"pdf_id": pdf_id,
|
|
153
|
+
"pdf_hash": str(pdf.pdf_hash),
|
|
154
|
+
},
|
|
155
|
+
status=status.HTTP_500_INTERNAL_SERVER_ERROR,
|
|
156
|
+
)
|