endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.9__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 +2 -11
- endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +3 -3
- endoreg_db/data/event_classification/data.yaml +4 -0
- endoreg_db/data/event_classification_choice/data.yaml +9 -0
- endoreg_db/data/examination/examinations/data.yaml +114 -14
- endoreg_db/data/examination/time-type/data.yaml +0 -3
- endoreg_db/data/examination_indication/endoscopy.yaml +108 -173
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +0 -70
- endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +33 -37
- endoreg_db/data/finding/00_generic.yaml +35 -0
- endoreg_db/data/finding/00_generic_complication.yaml +9 -0
- endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
- endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
- endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
- endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
- endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
- endoreg_db/data/finding_classification/00_generic.yaml +44 -0
- endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
- endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
- endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
- endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
- endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
- endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
- endoreg_db/data/finding_classification_choice/{yes_no_na.yaml → 00_generic.yaml} +5 -1
- endoreg_db/data/finding_classification_choice/{examination_setting_generic_types.yaml → 00_generic_baseline.yaml} +10 -2
- endoreg_db/data/finding_classification_choice/{complication_generic_types.yaml → 00_generic_complication.yaml} +1 -1
- endoreg_db/data/finding_classification_choice/{histology.yaml → 00_generic_histology.yaml} +1 -4
- endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
- endoreg_db/data/finding_classification_choice/{bowel_preparation.yaml → 02_colonoscopy_bowel_preparation.yaml} +1 -30
- endoreg_db/data/finding_classification_choice/{colonoscopy_not_complete_reason.yaml → 02_colonoscopy_generic.yaml} +1 -1
- endoreg_db/data/finding_classification_choice/{histology_polyp.yaml → 02_colonoscopy_histology.yaml} +1 -1
- endoreg_db/data/finding_classification_choice/{colonoscopy_location.yaml → 02_colonoscopy_location.yaml} +23 -4
- endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
- endoreg_db/data/finding_classification_choice/{colon_lesion_paris.yaml → 02_colonoscopy_polyp_morphology.yaml} +26 -8
- endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
- endoreg_db/data/finding_classification_type/{colonoscopy_basic.yaml → 00_generic.yaml} +18 -13
- endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
- endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
- endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
- endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
- endoreg_db/data/finding_type/data.yaml +8 -12
- endoreg_db/data/requirement/01_patient_data.yaml +93 -0
- endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
- endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
- endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +29 -12
- endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
- endoreg_db/data/requirement_set/{endoscopy_bleeding_risk.yaml → 02_endoscopy_bleeding_risk.yaml} +0 -6
- endoreg_db/data/requirement_set/90_coloreg.yaml +190 -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 +4 -2
- endoreg_db/forms/examination_form.py +1 -1
- endoreg_db/helpers/data_loader.py +125 -53
- endoreg_db/helpers/default_objects.py +116 -81
- endoreg_db/import_files/__init__.py +27 -0
- endoreg_db/import_files/context/__init__.py +7 -0
- endoreg_db/import_files/context/default_sensitive_meta.py +81 -0
- endoreg_db/import_files/context/ensure_center.py +17 -0
- endoreg_db/import_files/context/file_lock.py +66 -0
- endoreg_db/import_files/context/import_context.py +43 -0
- endoreg_db/import_files/context/validate_directories.py +56 -0
- endoreg_db/import_files/file_storage/__init__.py +15 -0
- endoreg_db/import_files/file_storage/create_report_file.py +76 -0
- endoreg_db/import_files/file_storage/create_video_file.py +75 -0
- endoreg_db/import_files/file_storage/sensitive_meta_storage.py +39 -0
- endoreg_db/import_files/file_storage/state_management.py +400 -0
- endoreg_db/import_files/file_storage/storage.py +36 -0
- endoreg_db/import_files/import_service.md +26 -0
- endoreg_db/import_files/processing/__init__.py +11 -0
- endoreg_db/import_files/processing/report_processing/report_anonymization.py +94 -0
- endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
- endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
- endoreg_db/import_files/processing/video_processing/video_cleanup_on_error.py +119 -0
- endoreg_db/import_files/pseudonymization/fake.py +52 -0
- endoreg_db/import_files/pseudonymization/k_anonymity.py +182 -0
- endoreg_db/import_files/pseudonymization/k_pseudonymity.py +128 -0
- endoreg_db/import_files/report_import_service.py +141 -0
- endoreg_db/import_files/video_import_service.py +150 -0
- 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_report.py +130 -65
- endoreg_db/management/commands/import_video.py +9 -10
- endoreg_db/management/commands/import_video_with_classification.py +2 -2
- endoreg_db/management/commands/list_routes.py +18 -0
- endoreg_db/management/commands/load_ai_model_data.py +5 -5
- endoreg_db/management/commands/load_ai_model_label_data.py +9 -7
- endoreg_db/management/commands/load_base_db_data.py +5 -134
- endoreg_db/management/commands/load_center_data.py +12 -12
- endoreg_db/management/commands/load_contraindication_data.py +14 -16
- endoreg_db/management/commands/load_disease_classification_choices_data.py +15 -18
- endoreg_db/management/commands/load_disease_classification_data.py +15 -18
- endoreg_db/management/commands/load_disease_data.py +25 -28
- endoreg_db/management/commands/load_endoscope_data.py +20 -27
- endoreg_db/management/commands/load_event_data.py +14 -16
- endoreg_db/management/commands/load_examination_data.py +31 -44
- endoreg_db/management/commands/load_examination_indication_data.py +20 -21
- endoreg_db/management/commands/load_finding_data.py +52 -80
- endoreg_db/management/commands/load_information_source.py +21 -23
- endoreg_db/management/commands/load_lab_value_data.py +17 -26
- endoreg_db/management/commands/load_medication_data.py +13 -12
- endoreg_db/management/commands/load_organ_data.py +15 -19
- endoreg_db/management/commands/load_pdf_type_data.py +19 -18
- endoreg_db/management/commands/load_profession_data.py +14 -17
- endoreg_db/management/commands/load_qualification_data.py +20 -23
- endoreg_db/management/commands/load_report_reader_flag_data.py +17 -19
- endoreg_db/management/commands/load_requirement_data.py +62 -39
- endoreg_db/management/commands/load_requirement_set_tags.py +95 -0
- endoreg_db/management/commands/load_risk_data.py +7 -6
- endoreg_db/management/commands/load_shift_data.py +20 -23
- endoreg_db/management/commands/load_tag_data.py +8 -11
- endoreg_db/management/commands/load_unit_data.py +17 -19
- endoreg_db/management/commands/setup_endoreg_db.py +3 -3
- endoreg_db/management/commands/start_filewatcher.py +46 -37
- endoreg_db/management/commands/storage_management.py +271 -203
- endoreg_db/management/commands/validate_video_files.py +1 -5
- endoreg_db/migrations/0001_initial.py +297 -250
- 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 +129 -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 +8 -9
- endoreg_db/models/label/annotation/image_classification.py +10 -9
- endoreg_db/models/label/annotation/video_segmentation_annotation.py +23 -28
- 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 +98 -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 +194 -194
- endoreg_db/models/media/pdf/report_file.py +25 -29
- endoreg_db/models/media/pdf/report_reader/report_reader_config.py +55 -47
- endoreg_db/models/media/pdf/report_reader/report_reader_flag.py +23 -7
- endoreg_db/models/media/processing_history/__init__.py +5 -0
- endoreg_db/models/media/processing_history/processing_history.py +96 -0
- endoreg_db/models/media/video/__init__.py +1 -0
- endoreg_db/models/media/video/create_from_file.py +139 -77
- endoreg_db/models/media/video/pipe_2.py +8 -9
- endoreg_db/models/media/video/video_file.py +174 -112
- 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 +113 -61
- 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/README.md +1 -0
- 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 +39 -20
- endoreg_db/models/medical/examination/examination_indication.py +30 -95
- endoreg_db/models/medical/examination/examination_time.py +23 -8
- 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 +32 -40
- endoreg_db/models/medical/finding/finding_classification.py +42 -72
- endoreg_db/models/medical/finding/finding_intervention.py +25 -22
- endoreg_db/models/medical/finding/finding_type.py +13 -12
- endoreg_db/models/medical/hardware/endoscope.py +26 -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 +6 -6
- 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 +125 -18
- endoreg_db/models/metadata/pdf_meta.py +31 -24
- endoreg_db/models/metadata/sensitive_meta.py +105 -85
- endoreg_db/models/metadata/sensitive_meta_logic.py +198 -103
- 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 +50 -29
- 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/report/report.py +6 -0
- endoreg_db/models/requirement/requirement.py +329 -361
- 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 +103 -112
- 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 +49 -51
- endoreg_db/models/state/label_video_segment.py +9 -0
- endoreg_db/models/state/raw_pdf.py +101 -68
- endoreg_db/models/state/sensitive_meta.py +6 -2
- endoreg_db/models/state/video.py +110 -90
- endoreg_db/models/upload_job.py +35 -34
- endoreg_db/models/utils.py +28 -25
- endoreg_db/queries/__init__.py +3 -1
- endoreg_db/root_urls.py +21 -2
- endoreg_db/schemas/examination_evaluation.py +1 -1
- endoreg_db/serializers/__init__.py +2 -10
- endoreg_db/serializers/anonymization.py +18 -10
- endoreg_db/serializers/label_video_segment/label_video_segment.py +2 -29
- endoreg_db/serializers/meta/__init__.py +1 -6
- endoreg_db/serializers/meta/sensitive_meta_detail.py +63 -118
- endoreg_db/serializers/misc/file_overview.py +11 -99
- endoreg_db/serializers/misc/sensitive_patient_data.py +50 -26
- endoreg_db/serializers/patient_examination/patient_examination.py +3 -3
- endoreg_db/serializers/pdf/anony_text_validation.py +39 -23
- endoreg_db/serializers/requirements/requirement_sets.py +92 -22
- endoreg_db/serializers/video/segmentation.py +2 -1
- endoreg_db/serializers/video/video_file_list.py +65 -34
- endoreg_db/serializers/video/video_processing_history.py +20 -5
- endoreg_db/services/__old/pdf_import.py +1487 -0
- endoreg_db/services/__old/video_import.py +1306 -0
- endoreg_db/services/anonymization.py +128 -89
- endoreg_db/services/lookup_service.py +65 -52
- endoreg_db/services/lookup_store.py +2 -2
- endoreg_db/services/pdf_import.py +0 -1382
- endoreg_db/services/report_import.py +10 -0
- endoreg_db/services/video_import.py +6 -1255
- endoreg_db/tasks/upload_tasks.py +79 -70
- endoreg_db/tasks/video_ingest.py +8 -4
- endoreg_db/urls/__init__.py +5 -32
- endoreg_db/urls/ai.py +32 -0
- endoreg_db/urls/media.py +121 -83
- 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 +142 -40
- endoreg_db/utils/defaults/set_default_center.py +32 -0
- endoreg_db/utils/names.py +22 -16
- endoreg_db/utils/paths.py +110 -46
- endoreg_db/utils/permissions.py +2 -1
- endoreg_db/utils/pipelines/Readme.md +1 -1
- endoreg_db/utils/pipelines/process_video_dir.py +1 -1
- endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +655 -0
- endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +97 -0
- 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 +85 -183
- endoreg_db/views/ai/__init__.py +8 -0
- endoreg_db/views/ai/label.py +155 -0
- endoreg_db/views/anonymization/media_management.py +202 -166
- endoreg_db/views/anonymization/overview.py +99 -67
- endoreg_db/views/anonymization/validate.py +182 -44
- endoreg_db/views/media/__init__.py +7 -20
- endoreg_db/views/media/pdf_media.py +197 -174
- endoreg_db/views/media/sensitive_metadata.py +193 -138
- endoreg_db/views/media/video_media.py +89 -82
- endoreg_db/views/meta/__init__.py +0 -8
- endoreg_db/views/misc/__init__.py +1 -7
- endoreg_db/views/misc/upload_views.py +94 -93
- endoreg_db/views/patient/patient.py +5 -4
- endoreg_db/views/report/__init__.py +5 -7
- endoreg_db/views/{pdf → report}/reimport.py +22 -22
- endoreg_db/views/{pdf/pdf_stream.py → report/report_stream.py} +46 -39
- endoreg_db/views/requirement/evaluate.py +188 -187
- endoreg_db/views/requirement/lookup.py +17 -3
- endoreg_db/views/requirement/lookup_store.py +22 -90
- endoreg_db/views/requirement/requirement_utils.py +89 -0
- endoreg_db/views/video/__init__.py +23 -24
- endoreg_db/views/video/correction.py +201 -172
- endoreg_db/views/video/reimport.py +1 -1
- endoreg_db/views/{media/video_segments.py → video/segments_crud.py} +77 -40
- endoreg_db/views/video/{video_meta.py → video_meta_stats.py} +2 -2
- endoreg_db/views/video/video_stream.py +7 -8
- {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/METADATA +7 -3
- {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/RECORD +391 -413
- {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/WHEEL +1 -1
- endoreg_db/data/finding/anatomy_colon.yaml +0 -128
- endoreg_db/data/finding/colonoscopy.yaml +0 -40
- endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +0 -56
- endoreg_db/data/finding/complication.yaml +0 -16
- endoreg_db/data/finding/data.yaml +0 -105
- endoreg_db/data/finding/examination_setting.yaml +0 -16
- endoreg_db/data/finding/medication_related.yaml +0 -18
- endoreg_db/data/finding/outcome.yaml +0 -12
- endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +0 -95
- endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +0 -22
- endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +0 -25
- endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
- endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
- endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +0 -68
- endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
- endoreg_db/data/finding_classification/colonoscopy_location.yaml +0 -80
- endoreg_db/data/finding_classification/colonoscopy_lst.yaml +0 -21
- endoreg_db/data/finding_classification/colonoscopy_nice.yaml +0 -20
- endoreg_db/data/finding_classification/colonoscopy_paris.yaml +0 -26
- endoreg_db/data/finding_classification/colonoscopy_sano.yaml +0 -22
- endoreg_db/data/finding_classification/colonoscopy_summary.yaml +0 -53
- endoreg_db/data/finding_classification/complication_generic.yaml +0 -25
- endoreg_db/data/finding_classification/examination_setting_generic.yaml +0 -40
- endoreg_db/data/finding_classification/histology_colo.yaml +0 -51
- endoreg_db/data/finding_classification/intervention_required.yaml +0 -26
- endoreg_db/data/finding_classification/medication_related.yaml +0 -23
- endoreg_db/data/finding_classification/visualized.yaml +0 -33
- endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
- endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
- endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
- endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +0 -15
- endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +0 -17
- endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
- endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +0 -14
- endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
- endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +0 -82
- endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
- endoreg_db/data/finding_classification_choice/outcome.yaml +0 -19
- endoreg_db/data/finding_intervention/endoscopy.yaml +0 -43
- endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
- endoreg_db/data/finding_intervention/endoscopy_egd.yaml +0 -128
- endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +0 -32
- endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +0 -9
- endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +0 -36
- endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +0 -79
- endoreg_db/data/requirement/age.yaml +0 -26
- endoreg_db/data/requirement/gender.yaml +0 -25
- endoreg_db/management/commands/init_default_ai_model.py +0 -112
- endoreg_db/management/commands/reset_celery_schedule.py +0 -9
- endoreg_db/management/commands/validate_video.py +0 -204
- endoreg_db/migrations/0002_add_video_correction_models.py +0 -52
- endoreg_db/migrations/0003_add_center_display_name.py +0 -30
- endoreg_db/models/administration/permissions/__init__.py +0 -44
- 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/renames.yml +0 -8
- endoreg_db/serializers/_old/raw_pdf_meta_validation.py +0 -223
- endoreg_db/serializers/_old/raw_video_meta_validation.py +0 -179
- endoreg_db/serializers/_old/video.py +0 -71
- endoreg_db/serializers/meta/pdf_file_meta_extraction.py +0 -115
- endoreg_db/serializers/meta/report_meta.py +0 -53
- endoreg_db/serializers/report/__init__.py +0 -9
- endoreg_db/serializers/report/mixins.py +0 -45
- endoreg_db/serializers/report/report.py +0 -105
- endoreg_db/serializers/report/report_list.py +0 -22
- endoreg_db/serializers/report/secure_file_url.py +0 -26
- endoreg_db/serializers/video/video_metadata.py +0 -105
- endoreg_db/services/requirements_object.py +0 -147
- endoreg_db/services/storage_aware_video_processor.py +0 -344
- endoreg_db/urls/files.py +0 -6
- endoreg_db/urls/label_video_segment_validate.py +0 -33
- endoreg_db/urls/label_video_segments.py +0 -46
- 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/utils/requirement_operator_logic/model_evaluators.py +0 -368
- endoreg_db/views/label/__init__.py +0 -5
- endoreg_db/views/label/label.py +0 -15
- endoreg_db/views/label_video_segment/__init__.py +0 -16
- endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +0 -44
- endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +0 -50
- endoreg_db/views/label_video_segment/label_video_segment.py +0 -77
- endoreg_db/views/label_video_segment/label_video_segment_by_label.py +0 -174
- endoreg_db/views/label_video_segment/label_video_segment_detail.py +0 -73
- endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +0 -46
- endoreg_db/views/label_video_segment/validate.py +0 -226
- endoreg_db/views/media/segments.py +0 -71
- endoreg_db/views/meta/available_files_list.py +0 -146
- endoreg_db/views/meta/report_meta.py +0 -53
- endoreg_db/views/meta/sensitive_meta_detail.py +0 -148
- endoreg_db/views/misc/secure_file_serving_view.py +0 -80
- endoreg_db/views/misc/secure_file_url_view.py +0 -84
- endoreg_db/views/misc/secure_url_validate.py +0 -79
- endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +0 -164
- endoreg_db/views/patient_finding_location/__init__.py +0 -5
- endoreg_db/views/patient_finding_location/pfl_create.py +0 -70
- endoreg_db/views/patient_finding_morphology/__init__.py +0 -5
- endoreg_db/views/patient_finding_morphology/pfm_create.py +0 -70
- endoreg_db/views/pdf/__init__.py +0 -8
- 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/segmentation.py +0 -274
- endoreg_db/views/video/task_status.py +0 -49
- endoreg_db/views/video/timeline.py +0 -46
- endoreg_db/views/video/video_analyze.py +0 -52
- endoreg_db/views.py +0 -0
- /endoreg_db/data/requirement/{colonoscopy_baseline_austria.yaml → old/colonoscopy_baseline_austria.yaml} +0 -0
- /endoreg_db/data/requirement/{disease_cardiovascular.yaml → old/disease_cardiovascular.yaml} +0 -0
- /endoreg_db/data/requirement/{disease_classification_choice_cardiovascular.yaml → old/disease_classification_choice_cardiovascular.yaml} +0 -0
- /endoreg_db/data/requirement/{disease_hepatology.yaml → old/disease_hepatology.yaml} +0 -0
- /endoreg_db/data/requirement/{disease_misc.yaml → old/disease_misc.yaml} +0 -0
- /endoreg_db/data/requirement/{disease_renal.yaml → old/disease_renal.yaml} +0 -0
- /endoreg_db/data/requirement/{endoscopy_bleeding_risk.yaml → old/endoscopy_bleeding_risk.yaml} +0 -0
- /endoreg_db/data/requirement/{event_cardiology.yaml → old/event_cardiology.yaml} +0 -0
- /endoreg_db/data/requirement/{event_requirements.yaml → old/event_requirements.yaml} +0 -0
- /endoreg_db/data/requirement/{finding_colon_polyp.yaml → old/finding_colon_polyp.yaml} +0 -0
- /endoreg_db/{migrations/__init__.py → data/requirement/old/gender.yaml} +0 -0
- /endoreg_db/data/requirement/{lab_value.yaml → old/lab_value.yaml} +0 -0
- /endoreg_db/data/requirement/{medication.yaml → old/medication.yaml} +0 -0
- /endoreg_db/data/requirement_operator/{age.yaml → _old/age.yaml} +0 -0
- /endoreg_db/data/requirement_operator/{lab_operators.yaml → _old/lab_operators.yaml} +0 -0
- /endoreg_db/data/requirement_operator/{model_operators.yaml → _old/model_operators.yaml} +0 -0
- /endoreg_db/{models/media/video/refactor_plan.md → import_files/pseudonymization/__init__.py} +0 -0
- /endoreg_db/{models/media/video/video_file_frames.py → import_files/pseudonymization/pseudonymize.py} +0 -0
- /endoreg_db/models/{metadata/frame_ocr_result.py → report/__init__.py} +0 -0
- /endoreg_db/{urls/sensitive_meta.py → models/report/images.py} +0 -0
- /endoreg_db/utils/requirement_operator_logic/{lab_value_operators.py → _old/lab_value_operators.py} +0 -0
- {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/licenses/LICENSE +0 -0
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Checks if a given date falls within the timeframe specified by a Requirement.
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def _evaluate_models_match_any(requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
|
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+
"""
|
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127
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+
Checks if the requirement_links matches any of the input_links.
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+
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+
Args:
|
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|
+
requirement_links: The reference set of requirement links to compare against.
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+
input_links: The aggregated requirement links from the input objects.
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+
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Returns:
|
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True if the input set of requirement links matches according to requirement_links.match_any; otherwise, False.
|
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+
"""
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+
return requirement_links.match_any(input_links)
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+
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+
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+
def _evaluate_models_match_any_in_timeframe(
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+
requirement_links: "RequirementLinks",
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+
input_links: "RequirementLinks",
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+
requirement: "Requirement", # Explicitly pass Requirement
|
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+
**kwargs, # Keep for consistency, though 'requirement' is the main one used here
|
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|
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) -> bool:
|
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+
"""
|
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+
Checks if any relevant model in input_links matches a model specified in
|
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+
requirement_links AND falls within the timeframe defined on the Requirement.
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+
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+
Currently focuses on PatientEvent instances and their dates.
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+
"""
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+
if not _has_timeframe_configuration(requirement):
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return False
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+
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+
active_req_links_dict = requirement_links.active()
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+
if not active_req_links_dict:
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+
# If the Requirement itself doesn't specify any models to match (e.g., requirement.events is empty),
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# then it's vacuously true that "any" of these (non-existent) required models are matched.
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# The timeframe aspect becomes irrelevant if no specific models are being checked.
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+
return True
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+
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+
# --- Handle PatientEvents ---
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# Check if the requirement is concerned with events
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if requirement_links.events: # This list contains Event model instances
|
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required_event_models = set(requirement_links.events) # Target Event models from the Requirement
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+
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# input_links.patient_events contains PatientEvent instances provided as input
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for patient_event_instance in input_links.patient_events:
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# Check if the event of the current PatientEvent instance is one of the target events
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if patient_event_instance.event in required_event_models:
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# If it is, check if this PatientEvent's date is within the timeframe
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if _is_date_in_timeframe(patient_event_instance.date, requirement):
|
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return True # Found a matching event within the timeframe
|
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+
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|
+
# --- Handle Other Model Types (Example: PatientLabValue) ---
|
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|
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# if requirement_links.lab_values:
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+
# required_lab_value_models = set(requirement_links.lab_values)
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|
+
# for plv_instance in input_links.patient_lab_values:
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+
# if plv_instance.lab_value in required_lab_value_models:
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|
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# date_to_check = None
|
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|
+
# if hasattr(plv_instance, 'date_time_value') and plv_instance.date_time_value:
|
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|
+
# date_to_check = plv_instance.date_time_value.date()
|
|
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|
+
# elif hasattr(plv_instance, 'date') and plv_instance.date: # If it had a simple date field
|
|
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|
+
# date_to_check = plv_instance.date
|
|
184
|
+
#
|
|
185
|
+
# if _is_date_in_timeframe(date_to_check, requirement):
|
|
186
|
+
# return True
|
|
187
|
+
|
|
188
|
+
# If the code reaches here, no matching model within the timeframe was found
|
|
189
|
+
# for any of the categories specified in requirement_links.
|
|
190
|
+
return False
|
|
191
|
+
|
|
192
|
+
|
|
193
|
+
def _evaluate_models_match_all_in_timeframe(
|
|
194
|
+
requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
|
|
195
|
+
) -> bool:
|
|
196
|
+
if not _evaluate_models_match_all(requirement_links, input_links, **kwargs):
|
|
197
|
+
return False
|
|
198
|
+
|
|
199
|
+
if not requirement_links.events:
|
|
200
|
+
return True
|
|
201
|
+
|
|
202
|
+
if not _has_timeframe_configuration(requirement):
|
|
203
|
+
return False
|
|
204
|
+
|
|
205
|
+
required_events = set(requirement_links.events)
|
|
206
|
+
patient_events = getattr(input_links, "patient_events", [])
|
|
207
|
+
if not patient_events:
|
|
208
|
+
return False
|
|
209
|
+
|
|
210
|
+
for event in required_events:
|
|
211
|
+
found_in_timeframe = False
|
|
212
|
+
for patient_event in patient_events:
|
|
213
|
+
if getattr(patient_event, "event", None) == event:
|
|
214
|
+
if _is_date_in_timeframe(getattr(patient_event, "date", None), requirement):
|
|
215
|
+
found_in_timeframe = True
|
|
216
|
+
break
|
|
217
|
+
if not found_in_timeframe:
|
|
218
|
+
return False
|
|
219
|
+
return True
|
|
220
|
+
|
|
221
|
+
if requirement.unit is None:
|
|
222
|
+
return False
|
|
223
|
+
|
|
224
|
+
|
|
225
|
+
def _evaluate_models_match_none_in_timeframe(
|
|
226
|
+
requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
|
|
227
|
+
) -> bool:
|
|
228
|
+
if not requirement_links.events:
|
|
229
|
+
return True
|
|
230
|
+
|
|
231
|
+
if not _has_timeframe_configuration(requirement):
|
|
232
|
+
return False
|
|
233
|
+
|
|
234
|
+
required_events = set(requirement_links.events)
|
|
235
|
+
for patient_event in getattr(input_links, "patient_events", []):
|
|
236
|
+
if getattr(patient_event, "event", None) in required_events:
|
|
237
|
+
if _is_date_in_timeframe(getattr(patient_event, "date", None), requirement):
|
|
238
|
+
return False
|
|
239
|
+
return True
|
|
240
|
+
|
|
241
|
+
|
|
242
|
+
def _evaluate_models_match_all(requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
|
|
243
|
+
"""
|
|
244
|
+
Evaluates if all active links in requirement_links are present in input_links.
|
|
245
|
+
|
|
246
|
+
For each category of links in requirement_links (e.g., diseases, examinations),
|
|
247
|
+
all items specified in that category in requirement_links must be present in the
|
|
248
|
+
corresponding category in input_links.
|
|
249
|
+
|
|
250
|
+
Args:
|
|
251
|
+
requirement_links: The RequirementLinks object from the Requirement model.
|
|
252
|
+
input_links: The aggregated RequirementLinks object from the input arguments.
|
|
253
|
+
**kwargs: Additional keyword arguments (currently unused).
|
|
254
|
+
|
|
255
|
+
Returns:
|
|
256
|
+
True if all specified items in requirement_links are found in input_links,
|
|
257
|
+
False otherwise.
|
|
258
|
+
"""
|
|
259
|
+
active_req_links = requirement_links.active() # Get dict of non-empty lists from requirement
|
|
260
|
+
|
|
261
|
+
if not active_req_links: # If the requirement specifies no actual items to link
|
|
262
|
+
return True # Vacuously true, as there are no conditions to fail
|
|
263
|
+
|
|
264
|
+
for link_category_name, req_items_list in active_req_links.items():
|
|
265
|
+
input_items_list = getattr(input_links, link_category_name, [])
|
|
266
|
+
|
|
267
|
+
try:
|
|
268
|
+
set_input_items = set(input_items_list)
|
|
269
|
+
set_req_items = set(req_items_list)
|
|
270
|
+
except TypeError:
|
|
271
|
+
for req_item in req_items_list:
|
|
272
|
+
if req_item not in input_items_list:
|
|
273
|
+
return False
|
|
274
|
+
continue
|
|
275
|
+
|
|
276
|
+
if not set_req_items.issubset(set_input_items):
|
|
277
|
+
return False
|
|
278
|
+
|
|
279
|
+
return True
|
|
280
|
+
|
|
281
|
+
|
|
282
|
+
def _evaluate_models_match_none(requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
|
|
283
|
+
"""Returns True when no required models are present in the input links."""
|
|
284
|
+
active_req_links = requirement_links.active()
|
|
285
|
+
if not active_req_links:
|
|
286
|
+
return True
|
|
287
|
+
|
|
288
|
+
for link_category_name, req_items_list in active_req_links.items():
|
|
289
|
+
input_items_list = getattr(input_links, link_category_name, [])
|
|
290
|
+
if not input_items_list:
|
|
291
|
+
continue
|
|
292
|
+
try:
|
|
293
|
+
if set(req_items_list) & set(input_items_list):
|
|
294
|
+
return False
|
|
295
|
+
except TypeError:
|
|
296
|
+
for req_item in req_items_list:
|
|
297
|
+
if req_item in input_items_list:
|
|
298
|
+
return False
|
|
299
|
+
return True
|
|
300
|
+
|
|
301
|
+
|
|
302
|
+
def _count_matching_models(
|
|
303
|
+
requirement_links: "RequirementLinks",
|
|
304
|
+
input_links: "RequirementLinks",
|
|
305
|
+
) -> int:
|
|
306
|
+
"""Counts how many required models are present in the input links."""
|
|
307
|
+
active_req_links = requirement_links.active()
|
|
308
|
+
if not active_req_links:
|
|
309
|
+
return 0
|
|
310
|
+
|
|
311
|
+
match_count = 0
|
|
312
|
+
for link_category_name, req_items_list in active_req_links.items():
|
|
313
|
+
input_items_list = getattr(input_links, link_category_name, [])
|
|
314
|
+
if not input_items_list:
|
|
315
|
+
continue
|
|
316
|
+
try:
|
|
317
|
+
match_count += len(set(req_items_list) & set(input_items_list))
|
|
318
|
+
except TypeError:
|
|
319
|
+
for req_item in req_items_list:
|
|
320
|
+
if req_item in input_items_list:
|
|
321
|
+
match_count += 1
|
|
322
|
+
return match_count
|
|
323
|
+
|
|
324
|
+
|
|
325
|
+
def _resolve_expected_count(requirement: "Requirement") -> int | None:
|
|
326
|
+
"""Extracts the expected count from numeric fields on the requirement."""
|
|
327
|
+
if requirement.numeric_value is not None:
|
|
328
|
+
return int(requirement.numeric_value)
|
|
329
|
+
if requirement.numeric_value_min is not None:
|
|
330
|
+
return int(requirement.numeric_value_min)
|
|
331
|
+
return None
|
|
332
|
+
|
|
333
|
+
|
|
334
|
+
def _has_timeframe_configuration(requirement: "Requirement") -> bool:
|
|
335
|
+
"""Checks whether timeframe boundaries and unit are configured."""
|
|
336
|
+
return (
|
|
337
|
+
requirement.unit is not None
|
|
338
|
+
and requirement.numeric_value_min is not None
|
|
339
|
+
and requirement.numeric_value_max is not None
|
|
340
|
+
and _normalize_timeframe_unit(requirement) is not None
|
|
341
|
+
)
|
|
342
|
+
|
|
343
|
+
|
|
344
|
+
def _count_matching_events_in_timeframe(
|
|
345
|
+
requirement_links: "RequirementLinks",
|
|
346
|
+
input_links: "RequirementLinks",
|
|
347
|
+
requirement: "Requirement",
|
|
348
|
+
) -> int:
|
|
349
|
+
"""Counts required events that have a matching patient event within the timeframe."""
|
|
350
|
+
required_events = set(requirement_links.events)
|
|
351
|
+
if not required_events:
|
|
352
|
+
return 0
|
|
353
|
+
|
|
354
|
+
patient_events = getattr(input_links, "patient_events", [])
|
|
355
|
+
if not patient_events:
|
|
356
|
+
return 0
|
|
357
|
+
|
|
358
|
+
matched_events = 0
|
|
359
|
+
for event in required_events:
|
|
360
|
+
for patient_event in patient_events:
|
|
361
|
+
if getattr(patient_event, "event", None) != event:
|
|
362
|
+
continue
|
|
363
|
+
if _is_date_in_timeframe(getattr(patient_event, "date", None), requirement):
|
|
364
|
+
matched_events += 1
|
|
365
|
+
break
|
|
366
|
+
return matched_events
|
|
367
|
+
|
|
368
|
+
|
|
369
|
+
def _evaluate_models_match_n(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
370
|
+
expected = _resolve_expected_count(requirement)
|
|
371
|
+
if expected is None:
|
|
372
|
+
return False
|
|
373
|
+
return _count_matching_models(requirement_links, input_links) == expected
|
|
374
|
+
|
|
375
|
+
|
|
376
|
+
def _evaluate_models_match_n_or_more(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
377
|
+
threshold = _resolve_expected_count(requirement)
|
|
378
|
+
if threshold is None:
|
|
379
|
+
return False
|
|
380
|
+
return _count_matching_models(requirement_links, input_links) >= max(threshold, 0)
|
|
381
|
+
|
|
382
|
+
|
|
383
|
+
def _evaluate_models_match_n_or_less(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
384
|
+
limit = _resolve_expected_count(requirement)
|
|
385
|
+
if limit is None:
|
|
386
|
+
return False
|
|
387
|
+
return _count_matching_models(requirement_links, input_links) <= limit
|
|
388
|
+
|
|
389
|
+
|
|
390
|
+
def _evaluate_models_match_count_in_range(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
391
|
+
if requirement.numeric_value_min is None or requirement.numeric_value_max is None:
|
|
392
|
+
return False
|
|
393
|
+
|
|
394
|
+
lower = int(requirement.numeric_value_min)
|
|
395
|
+
upper = int(requirement.numeric_value_max)
|
|
396
|
+
if lower > upper:
|
|
397
|
+
lower, upper = upper, lower
|
|
398
|
+
|
|
399
|
+
match_count = _count_matching_models(requirement_links, input_links)
|
|
400
|
+
return lower <= match_count <= upper
|
|
401
|
+
|
|
402
|
+
|
|
403
|
+
def _evaluate_models_match_n_in_timeframe(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
404
|
+
if not _has_timeframe_configuration(requirement):
|
|
405
|
+
return False
|
|
406
|
+
|
|
407
|
+
expected = _resolve_expected_count(requirement)
|
|
408
|
+
if expected is None:
|
|
409
|
+
return False
|
|
410
|
+
|
|
411
|
+
return _count_matching_events_in_timeframe(requirement_links, input_links, requirement) == expected
|
|
412
|
+
|
|
413
|
+
|
|
414
|
+
def _evaluate_models_match_n_or_more_in_timeframe(
|
|
415
|
+
requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
|
|
416
|
+
) -> bool:
|
|
417
|
+
if not _has_timeframe_configuration(requirement):
|
|
418
|
+
return False
|
|
419
|
+
|
|
420
|
+
threshold = _resolve_expected_count(requirement)
|
|
421
|
+
if threshold is None:
|
|
422
|
+
return False
|
|
423
|
+
|
|
424
|
+
return _count_matching_events_in_timeframe(requirement_links, input_links, requirement) >= max(threshold, 0)
|
|
425
|
+
|
|
426
|
+
|
|
427
|
+
def _evaluate_models_match_n_or_less_in_timeframe(
|
|
428
|
+
requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
|
|
429
|
+
) -> bool:
|
|
430
|
+
if not _has_timeframe_configuration(requirement):
|
|
431
|
+
return False
|
|
432
|
+
|
|
433
|
+
limit = _resolve_expected_count(requirement)
|
|
434
|
+
if limit is None:
|
|
435
|
+
return False
|
|
436
|
+
|
|
437
|
+
return _count_matching_events_in_timeframe(requirement_links, input_links, requirement) <= limit
|
|
438
|
+
|
|
439
|
+
|
|
440
|
+
def _evaluate_age_gte(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
441
|
+
"""
|
|
442
|
+
Checks if any patient in the input has an age greater than or equal to the requirement's numeric_value.
|
|
443
|
+
|
|
444
|
+
Args:
|
|
445
|
+
requirement_links: The RequirementLinks object from the Requirement model (not used for age checks).
|
|
446
|
+
input_links: The aggregated RequirementLinks object from the input arguments.
|
|
447
|
+
requirement: The Requirement instance containing the minimum age in numeric_value.
|
|
448
|
+
**kwargs: Additional keyword arguments, should contain 'original_input_args' with the original Patient instances.
|
|
449
|
+
|
|
450
|
+
Returns:
|
|
451
|
+
True if any patient in the input has an age >= requirement.numeric_value, False otherwise.
|
|
452
|
+
"""
|
|
453
|
+
import logging
|
|
454
|
+
|
|
455
|
+
from endoreg_db.models.administration.person.patient import Patient
|
|
456
|
+
|
|
457
|
+
logger = logging.getLogger(__name__)
|
|
458
|
+
|
|
459
|
+
if requirement.numeric_value is None:
|
|
460
|
+
logger.debug("age_gte: requirement.numeric_value is None, returning False")
|
|
461
|
+
return False # Cannot evaluate without a minimum age requirement
|
|
462
|
+
|
|
463
|
+
min_age = requirement.numeric_value
|
|
464
|
+
logger.debug(f"age_gte: Checking if any patient has age >= {min_age}")
|
|
465
|
+
|
|
466
|
+
# Check if we have Patient instances in the original_input_args
|
|
467
|
+
original_args = kwargs.get("original_input_args", [])
|
|
468
|
+
logger.debug(f"age_gte: Found {len(original_args)} original input arguments: {[type(arg).__name__ for arg in original_args]}")
|
|
469
|
+
|
|
470
|
+
for i, arg in enumerate(original_args):
|
|
471
|
+
logger.debug(f"age_gte: Checking argument {i}: {type(arg).__name__}")
|
|
472
|
+
if isinstance(arg, Patient):
|
|
473
|
+
patient_age = arg.age()
|
|
474
|
+
logger.debug(f"age_gte: Patient {arg} has age {patient_age}, comparing with min_age {min_age}")
|
|
475
|
+
if patient_age is not None and patient_age >= min_age:
|
|
476
|
+
logger.debug(f"age_gte: Patient age {patient_age} >= {min_age}, returning True")
|
|
477
|
+
return True
|
|
478
|
+
else:
|
|
479
|
+
logger.debug(f"age_gte: Patient age {patient_age} < {min_age} or is None")
|
|
480
|
+
# Handle QuerySets of patients
|
|
481
|
+
elif hasattr(arg, "model") and issubclass(arg.model, Patient):
|
|
482
|
+
logger.debug(f"age_gte: Found Patient QuerySet with {arg.count()} patients")
|
|
483
|
+
for patient in arg:
|
|
484
|
+
patient_age = patient.age()
|
|
485
|
+
logger.debug(f"age_gte: Patient {patient} has age {patient_age}, comparing with min_age {min_age}")
|
|
486
|
+
if patient_age is not None and patient_age >= min_age:
|
|
487
|
+
logger.debug(f"age_gte: Patient age {patient_age} >= {min_age}, returning True")
|
|
488
|
+
return True
|
|
489
|
+
else:
|
|
490
|
+
logger.debug(f"age_gte: Argument {i} is not a Patient or Patient QuerySet: {type(arg)}")
|
|
491
|
+
|
|
492
|
+
logger.debug(f"age_gte: No patient found with age >= {min_age}, returning False")
|
|
493
|
+
return False
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
def _evaluate_age_lte(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
|
|
497
|
+
"""
|
|
498
|
+
Checks if any patient in the input has an age less than or equal to the requirement's numeric_value.
|
|
499
|
+
|
|
500
|
+
Args:
|
|
501
|
+
requirement_links: The RequirementLinks object from the Requirement model (not used for age checks).
|
|
502
|
+
input_links: The aggregated RequirementLinks object from the input arguments.
|
|
503
|
+
requirement: The Requirement instance containing the maximum age in numeric_value.
|
|
504
|
+
**kwargs: Additional keyword arguments, should contain 'original_input_args' with the original Patient instances.
|
|
505
|
+
|
|
506
|
+
Returns:
|
|
507
|
+
True if any patient in the input has an age <= requirement.numeric_value, False otherwise.
|
|
508
|
+
"""
|
|
509
|
+
from endoreg_db.models.administration.person.patient import Patient
|
|
510
|
+
|
|
511
|
+
if requirement.numeric_value is None:
|
|
512
|
+
return False # Cannot evaluate without a maximum age requirement
|
|
513
|
+
|
|
514
|
+
max_age = requirement.numeric_value
|
|
515
|
+
|
|
516
|
+
# Check if we have Patient instances in the original_input_args
|
|
517
|
+
original_args = kwargs.get("original_input_args", [])
|
|
518
|
+
for arg in original_args:
|
|
519
|
+
if isinstance(arg, Patient):
|
|
520
|
+
patient_age = arg.age()
|
|
521
|
+
if patient_age is not None and patient_age <= max_age:
|
|
522
|
+
return True
|
|
523
|
+
# Handle QuerySets of patients
|
|
524
|
+
elif hasattr(arg, "model") and issubclass(arg.model, Patient):
|
|
525
|
+
for patient in arg:
|
|
526
|
+
patient_age = patient.age()
|
|
527
|
+
if patient_age is not None and patient_age <= max_age:
|
|
528
|
+
return True
|
|
529
|
+
|
|
530
|
+
return False
|
|
531
|
+
|
|
532
|
+
|
|
533
|
+
def dispatch_operator_evaluation(operator_name: str, requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
|
|
534
|
+
"""
|
|
535
|
+
Dispatches the evaluation to the appropriate function based on the operator name.
|
|
536
|
+
|
|
537
|
+
Args:
|
|
538
|
+
operator_name: The name of the operator to evaluate.
|
|
539
|
+
requirement_links: The RequirementLinks object from the Requirement model.
|
|
540
|
+
input_links: The aggregated RequirementLinks object from the input arguments.
|
|
541
|
+
**kwargs: Additional keyword arguments for specific operator logic.
|
|
542
|
+
For lab value operators, this includes 'requirement' (the Requirement model instance).
|
|
543
|
+
|
|
544
|
+
Returns:
|
|
545
|
+
True if the condition defined by the operator is met, False otherwise.
|
|
546
|
+
|
|
547
|
+
Raises:
|
|
548
|
+
NotImplementedError: If the evaluation logic for the operator's name is not implemented.
|
|
549
|
+
"""
|
|
550
|
+
from endoreg_db.models.requirement.requirement import Requirement # Runtime import for isinstance
|
|
551
|
+
|
|
552
|
+
from .lab_value_operators import LAB_VALUE_OPERATOR_FUNCTIONS
|
|
553
|
+
|
|
554
|
+
eval_func = None
|
|
555
|
+
requirement = kwargs.get("requirement") # Get requirement for operators that need it
|
|
556
|
+
|
|
557
|
+
def _kwargs_without_requirement() -> dict:
|
|
558
|
+
return {k: v for k, v in kwargs.items() if k != "requirement"}
|
|
559
|
+
|
|
560
|
+
if operator_name == "models_match_any":
|
|
561
|
+
eval_func = _evaluate_models_match_any
|
|
562
|
+
return eval_func(requirement_links=requirement_links, input_links=input_links, **kwargs)
|
|
563
|
+
elif operator_name == "models_match_all":
|
|
564
|
+
eval_func = _evaluate_models_match_all
|
|
565
|
+
return eval_func(requirement_links=requirement_links, input_links=input_links, **kwargs)
|
|
566
|
+
elif operator_name == "models_match_none":
|
|
567
|
+
eval_func = _evaluate_models_match_none
|
|
568
|
+
return eval_func(requirement_links=requirement_links, input_links=input_links, **kwargs)
|
|
569
|
+
elif operator_name == "models_match_any_in_timeframe":
|
|
570
|
+
# 'requirement' is already extracted from kwargs via requirement = kwargs.get("requirement")
|
|
571
|
+
if not isinstance(requirement, Requirement): # Ensure requirement is present and correct type
|
|
572
|
+
raise ValueError("models_match_any_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
573
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
574
|
+
eval_func = _evaluate_models_match_any_in_timeframe
|
|
575
|
+
return eval_func(
|
|
576
|
+
requirement_links=requirement_links,
|
|
577
|
+
input_links=input_links,
|
|
578
|
+
requirement=requirement, # Pass the requirement instance explicitly
|
|
579
|
+
**kwargs_for_eval, # Pass the remaining kwargs
|
|
580
|
+
)
|
|
581
|
+
elif operator_name == "models_match_all_in_timeframe":
|
|
582
|
+
if not isinstance(requirement, Requirement):
|
|
583
|
+
raise ValueError("models_match_all_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
584
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
585
|
+
return _evaluate_models_match_all_in_timeframe(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
586
|
+
elif operator_name == "models_match_none_in_timeframe":
|
|
587
|
+
if not isinstance(requirement, Requirement):
|
|
588
|
+
raise ValueError("models_match_none_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
589
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
590
|
+
return _evaluate_models_match_none_in_timeframe(
|
|
591
|
+
requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval
|
|
592
|
+
)
|
|
593
|
+
elif operator_name == "models_match_n":
|
|
594
|
+
if not isinstance(requirement, Requirement):
|
|
595
|
+
raise ValueError("models_match_n operator requires a valid 'requirement' instance in kwargs.")
|
|
596
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
597
|
+
return _evaluate_models_match_n(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
598
|
+
elif operator_name == "models_match_n_or_more":
|
|
599
|
+
if not isinstance(requirement, Requirement):
|
|
600
|
+
raise ValueError("models_match_n_or_more operator requires a valid 'requirement' instance in kwargs.")
|
|
601
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
602
|
+
return _evaluate_models_match_n_or_more(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
603
|
+
elif operator_name == "models_match_n_or_less":
|
|
604
|
+
if not isinstance(requirement, Requirement):
|
|
605
|
+
raise ValueError("models_match_n_or_less operator requires a valid 'requirement' instance in kwargs.")
|
|
606
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
607
|
+
return _evaluate_models_match_n_or_less(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
608
|
+
elif operator_name == "models_match_count_in_range":
|
|
609
|
+
if not isinstance(requirement, Requirement):
|
|
610
|
+
raise ValueError("models_match_count_in_range operator requires a valid 'requirement' instance in kwargs.")
|
|
611
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
612
|
+
return _evaluate_models_match_count_in_range(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
613
|
+
elif operator_name == "models_match_n_in_timeframe":
|
|
614
|
+
if not isinstance(requirement, Requirement):
|
|
615
|
+
raise ValueError("models_match_n_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
616
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
617
|
+
return _evaluate_models_match_n_in_timeframe(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
618
|
+
elif operator_name == "models_match_n_or_more_in_timeframe":
|
|
619
|
+
if not isinstance(requirement, Requirement):
|
|
620
|
+
raise ValueError("models_match_n_or_more_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
621
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
622
|
+
return _evaluate_models_match_n_or_more_in_timeframe(
|
|
623
|
+
requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval
|
|
624
|
+
)
|
|
625
|
+
elif operator_name == "models_match_n_or_less_in_timeframe":
|
|
626
|
+
if not isinstance(requirement, Requirement):
|
|
627
|
+
raise ValueError("models_match_n_or_less_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
628
|
+
kwargs_for_eval = _kwargs_without_requirement()
|
|
629
|
+
return _evaluate_models_match_n_or_less_in_timeframe(
|
|
630
|
+
requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval
|
|
631
|
+
)
|
|
632
|
+
elif operator_name in LAB_VALUE_OPERATOR_FUNCTIONS:
|
|
633
|
+
if not isinstance(requirement, Requirement): # Ensure requirement is present and correct type
|
|
634
|
+
raise ValueError(f"Lab value operator '{operator_name}' requires a valid 'requirement' instance in kwargs.")
|
|
635
|
+
|
|
636
|
+
eval_func = LAB_VALUE_OPERATOR_FUNCTIONS[operator_name]
|
|
637
|
+
return eval_func(input_links=input_links, requirement=requirement, operator_kwargs=kwargs)
|
|
638
|
+
elif operator_name == "age_gte":
|
|
639
|
+
if not isinstance(requirement, Requirement):
|
|
640
|
+
raise ValueError("age_gte operator requires a valid 'requirement' instance in kwargs.")
|
|
641
|
+
|
|
642
|
+
# Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice
|
|
643
|
+
kwargs_for_eval = {k: v for k, v in kwargs.items() if k != "requirement"}
|
|
644
|
+
|
|
645
|
+
return _evaluate_age_gte(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
646
|
+
elif operator_name == "age_lte":
|
|
647
|
+
if not isinstance(requirement, Requirement):
|
|
648
|
+
raise ValueError("age_lte operator requires a valid 'requirement' instance in kwargs.")
|
|
649
|
+
|
|
650
|
+
# Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice
|
|
651
|
+
kwargs_for_eval = {k: v for k, v in kwargs.items() if k != "requirement"}
|
|
652
|
+
|
|
653
|
+
return _evaluate_age_lte(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
|
|
654
|
+
else:
|
|
655
|
+
raise NotImplementedError(f"Evaluation logic for operator '{operator_name}' is not implemented.")
|