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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class CaseGenerator:
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"""
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Provides methods to generate cases based on a template.
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"""
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def __init__(self, template: CaseTemplate = None):
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"""
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Initializes the CaseGenerator with a template.
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Args:
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template (CaseTemplate, optional): The template to use for case generation. Defaults to the predefined template.
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"""
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self.template = template or CaseTemplate.objects.get(name=DEFAULT_CASE_TEMPLATE_NAME)
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self.lab_sample_factory = LabSampleFactory()
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# Define available rule types
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rule_type_names = [
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"create-object",
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"set-field-default",
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"set-field-by-distribution",
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"set-field-by-value",
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"set-field-single-choice",
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"set-field-multiple-choice",
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]
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self.available_rule_types = CaseTemplateRuleType.objects.filter(name__in=rule_type_names)
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def _validate_rule_type(self, rule_type: CaseTemplateRuleType):
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"""
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Validates if the rule type is supported.
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Args:
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rule_type (CaseTemplateRuleType): The rule type to validate.
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Raises:
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ValueError: If the rule type is not supported.
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"""
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if rule_type not in self.available_rule_types:
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raise ValueError(f"Rule type {rule_type} is not supported.")
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def _apply_create_object(self, rule: CaseTemplateRule, parent=None):
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"""
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Applies a create-object rule to generate a model instance.
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Args:
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rule (CaseTemplateRule): The rule to apply.
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parent (Optional[Model]): The parent object for the rule.
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Returns:
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Model: The created model instance.
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"""
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target_model = rule.get_target_model()
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extra_params = rule.extra_parameters or {}
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create_method_info = extra_params.get("create_method", {})
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assert create_method_info, "Create method must be set for a create-object rule."
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create_method = getattr(target_model, create_method_info["name"])
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kwargs = create_method_info.get("kwargs", {})
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if parent:
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kwargs[rule.parent_field] = parent
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target_instance = create_method(**kwargs)
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target_instance.save()
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for action in extra_params.get("actions", []):
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action_method = getattr(target_instance, action["name"])
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action_kwargs = action.get("kwargs", {})
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action_method(**action_kwargs)
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for chained_rule in rule.chained_rules.all():
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self.apply_rule(chained_rule, parent=target_instance)
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return target_instance
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def _apply_set_field_by_distribution(self, rule: CaseTemplateRule, parent):
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"""
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Applies a set-field-by-distribution rule.
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Args:
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rule (CaseTemplateRule): The rule to apply.
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parent (Model): The parent object for the rule.
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Returns:
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Model: The updated parent object.
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"""
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assert parent, "Parent must be provided for set-field-by-distribution rules."
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assert rule.target_field, "Target field must be specified for the rule."
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distribution = rule.get_distribution()
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value = distribution.generate_value()
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setattr(parent, rule.target_field, value)
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parent.save()
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return parent
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def apply_rule(self, rule: CaseTemplateRule, parent=None):
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"""
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Applies a rule based on its type to generate a case.
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Args:
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rule (CaseTemplateRule): The rule to apply.
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parent (Optional[Model]): The parent object for the rule.
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Returns:
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Model: The case by applying the rule.
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"""
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self._validate_rule_type(rule.rule_type)
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if rule.rule_type.name == "create-object":
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return self._apply_create_object(rule, parent)
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if rule.rule_type.name == "set-field-by-distribution":
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return self._apply_set_field_by_distribution(rule, parent)
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raise ValueError(f"Unsupported rule type: {rule.rule_type.name}")
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|
|
123
|
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def generate_case(self, case_template: CaseTemplate = None):
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"""
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Generates a case based on the provided or default template.
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Args:
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case_template (CaseTemplate, optional): The template to use for case generation. Defaults to None.
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Returns:
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Tuple[Model, Model]: The generated patient and medication schedule.
|
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|
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"""
|
|
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|
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case_template = case_template or CaseTemplate.objects.get(name=DEFAULT_CASE_TEMPLATE_NAME)
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|
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|
|
135
|
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create_patient_rule = case_template.get_create_patient_rule()
|
|
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|
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patient = self.apply_rule(create_patient_rule)
|
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|
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|
|
138
|
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medication_schedule_rule = case_template.get_create_patient_medication_schedule_rule()
|
|
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|
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medication_schedule = self.apply_rule(medication_schedule_rule, parent=patient)
|
|
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|
-
|
|
141
|
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return patient, medication_schedule
|
|
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|
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|
|
143
|
-
# if not create_new_patient:
|
|
144
|
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# raise NotImplementedError("Only new patients are supported at the moment.")
|
|
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|
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# else:
|
|
146
|
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# # TODO Implement patient rules
|
|
147
|
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# patient_rules = None # all rules of type "create_patient"
|
|
148
|
-
# patient = self.generate_patient(patient_rules)
|
|
149
|
-
|
|
150
|
-
# # Generate case based on template
|
|
151
|
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# rules = self.template.get_rules()
|
|
152
|
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# chained_rules = set()
|
|
153
|
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|
|
154
|
-
# for rule in rules:
|
|
155
|
-
# rule_chain = rule.get_all_downward_chained_rules()
|
|
156
|
-
# chained_rules.add(rule)
|
|
157
|
-
# chained_rules.update(rule_chain)
|
|
158
|
-
|
|
159
|
-
# return chained_rules
|
|
@@ -1,30 +0,0 @@
|
|
|
1
|
-
from endoreg_db.models import CaseTemplate
|
|
2
|
-
from endoreg_db.case_generator.case_generator import CaseGenerator
|
|
3
|
-
|
|
4
|
-
# TEMPLATE_NAME = "pre_endo-anticoagulation-af-low_risk"
|
|
5
|
-
TEMPLATE_NAME = "pre_default_screening_colonoscopy"
|
|
6
|
-
|
|
7
|
-
def fetch_template(template_name: str = DEFAULT_TEMPLATE_NAME) -> CaseTemplate:
|
|
8
|
-
"""
|
|
9
|
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Fetches a CaseTemplate by name.
|
|
10
|
-
|
|
11
|
-
Args:
|
|
12
|
-
template_name (str): The name of the template to fetch. Defaults to DEFAULT_TEMPLATE_NAME.
|
|
13
|
-
|
|
14
|
-
Returns:
|
|
15
|
-
CaseTemplate: The fetched CaseTemplate instance.
|
|
16
|
-
"""
|
|
17
|
-
return CaseTemplate.objects.get(name=template_name)
|
|
18
|
-
|
|
19
|
-
def initialize_case_generator(template_name: str = DEFAULT_TEMPLATE_NAME) -> CaseGenerator:
|
|
20
|
-
"""
|
|
21
|
-
Initializes a CaseGenerator with the specified template.
|
|
22
|
-
|
|
23
|
-
Args:
|
|
24
|
-
template_name (str): The name of the template to use. Defaults to DEFAULT_TEMPLATE_NAME.
|
|
25
|
-
|
|
26
|
-
Returns:
|
|
27
|
-
CaseGenerator: An instance of CaseGenerator initialized with the template.
|
|
28
|
-
"""
|
|
29
|
-
template = fetch_template(template_name)
|
|
30
|
-
return CaseGenerator(template)
|
|
@@ -1,368 +0,0 @@
|
|
|
1
|
-
import datetime # Add import
|
|
2
|
-
from datetime import timedelta # Add import
|
|
3
|
-
from typing import TYPE_CHECKING
|
|
4
|
-
|
|
5
|
-
if TYPE_CHECKING:
|
|
6
|
-
from endoreg_db.utils.links.requirement_link import RequirementLinks
|
|
7
|
-
from endoreg_db.models.requirement.requirement import Requirement
|
|
8
|
-
# from endoreg_db.models import Unit # Potentially needed for dynamic unit handling
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
# Helper function to check if a date is within the timeframe specified by a Requirement
|
|
12
|
-
def _is_date_in_timeframe(date_to_check: datetime.date | None, requirement: "Requirement") -> bool:
|
|
13
|
-
"""
|
|
14
|
-
Checks if a given date falls within the timeframe specified by a Requirement.
|
|
15
|
-
|
|
16
|
-
The timeframe is defined by `numeric_value_min` and `numeric_value_max` on the
|
|
17
|
-
Requirement, interpreted relative to the current date.
|
|
18
|
-
|
|
19
|
-
Currently, this function only supports timeframes specified in "days".
|
|
20
|
-
If the Requirement's unit is not "days", a NotImplementedError will be raised.
|
|
21
|
-
|
|
22
|
-
Args:
|
|
23
|
-
date_to_check: The date to evaluate. If None, returns False.
|
|
24
|
-
requirement: The Requirement instance containing timeframe definitions
|
|
25
|
-
(unit, numeric_value_min, numeric_value_max).
|
|
26
|
-
|
|
27
|
-
Returns:
|
|
28
|
-
True if the date_to_check is within the defined timeframe, False otherwise.
|
|
29
|
-
Returns False if date_to_check is None or if the requirement lacks
|
|
30
|
-
necessary timeframe information (unit, min/max values).
|
|
31
|
-
|
|
32
|
-
Raises:
|
|
33
|
-
NotImplementedError: If the requirement.unit.name is not 'days' (case-insensitive).
|
|
34
|
-
"""
|
|
35
|
-
if date_to_check is None:
|
|
36
|
-
return False
|
|
37
|
-
if not requirement.unit or requirement.numeric_value_min is None or requirement.numeric_value_max is None:
|
|
38
|
-
return False # Not enough information for timeframe evaluation
|
|
39
|
-
|
|
40
|
-
# For now, primarily supporting 'days'. Extend if other units are common.
|
|
41
|
-
if requirement.unit.name.lower() != "days":
|
|
42
|
-
raise NotImplementedError(
|
|
43
|
-
f"Timeframe unit '{requirement.unit.name}' is not supported. "
|
|
44
|
-
"Currently, only 'days' is implemented for timeframe checks."
|
|
45
|
-
)
|
|
46
|
-
|
|
47
|
-
today = datetime.date.today()
|
|
48
|
-
# numeric_value_min is typically negative for "days ago" (e.g., -30 for 30 days ago)
|
|
49
|
-
# numeric_value_max is typically 0 for "today"
|
|
50
|
-
timeframe_start_delta = int(requirement.numeric_value_min)
|
|
51
|
-
timeframe_end_delta = int(requirement.numeric_value_max)
|
|
52
|
-
|
|
53
|
-
start_date_bound = today + timedelta(days=timeframe_start_delta)
|
|
54
|
-
end_date_bound = today + timedelta(days=timeframe_end_delta)
|
|
55
|
-
|
|
56
|
-
return start_date_bound <= date_to_check <= end_date_bound
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
def _evaluate_models_match_any(
|
|
60
|
-
requirement_links: "RequirementLinks",
|
|
61
|
-
input_links: "RequirementLinks",
|
|
62
|
-
**kwargs
|
|
63
|
-
) -> bool:
|
|
64
|
-
"""
|
|
65
|
-
Checks if the requirement_links matches any of the input_links.
|
|
66
|
-
|
|
67
|
-
Args:
|
|
68
|
-
requirement_links: The reference set of requirement links to compare against.
|
|
69
|
-
input_links: The aggregated requirement links from the input objects.
|
|
70
|
-
|
|
71
|
-
Returns:
|
|
72
|
-
True if the input set of requirement links matches according to requirement_links.match_any; otherwise, False.
|
|
73
|
-
"""
|
|
74
|
-
return requirement_links.match_any(input_links)
|
|
75
|
-
|
|
76
|
-
|
|
77
|
-
def _evaluate_models_match_any_in_timeframe(
|
|
78
|
-
requirement_links: "RequirementLinks",
|
|
79
|
-
input_links: "RequirementLinks",
|
|
80
|
-
requirement: "Requirement", # Explicitly pass Requirement
|
|
81
|
-
**kwargs # Keep for consistency, though 'requirement' is the main one used here
|
|
82
|
-
) -> bool:
|
|
83
|
-
"""
|
|
84
|
-
Checks if any relevant model in input_links matches a model specified in
|
|
85
|
-
requirement_links AND falls within the timeframe defined on the Requirement.
|
|
86
|
-
|
|
87
|
-
Currently focuses on PatientEvent instances and their dates.
|
|
88
|
-
"""
|
|
89
|
-
active_req_links_dict = requirement_links.active()
|
|
90
|
-
if not active_req_links_dict:
|
|
91
|
-
# If the Requirement itself doesn't specify any models to match (e.g., requirement.events is empty),
|
|
92
|
-
# then it's vacuously true that "any" of these (non-existent) required models are matched.
|
|
93
|
-
# The timeframe aspect becomes irrelevant if no specific models are being checked.
|
|
94
|
-
return True
|
|
95
|
-
|
|
96
|
-
# --- Handle PatientEvents ---
|
|
97
|
-
# Check if the requirement is concerned with events
|
|
98
|
-
if requirement_links.events: # This list contains Event model instances
|
|
99
|
-
required_event_models = set(requirement_links.events) # Target Event models from the Requirement
|
|
100
|
-
|
|
101
|
-
# input_links.patient_events contains PatientEvent instances provided as input
|
|
102
|
-
for patient_event_instance in input_links.patient_events:
|
|
103
|
-
# Check if the event of the current PatientEvent instance is one of the target events
|
|
104
|
-
if patient_event_instance.event in required_event_models:
|
|
105
|
-
# If it is, check if this PatientEvent's date is within the timeframe
|
|
106
|
-
if _is_date_in_timeframe(patient_event_instance.date, requirement):
|
|
107
|
-
return True # Found a matching event within the timeframe
|
|
108
|
-
|
|
109
|
-
# --- Handle Other Model Types (Example: PatientLabValue) ---
|
|
110
|
-
# if requirement_links.lab_values:
|
|
111
|
-
# required_lab_value_models = set(requirement_links.lab_values)
|
|
112
|
-
# for plv_instance in input_links.patient_lab_values:
|
|
113
|
-
# if plv_instance.lab_value in required_lab_value_models:
|
|
114
|
-
# date_to_check = None
|
|
115
|
-
# if hasattr(plv_instance, 'date_time_value') and plv_instance.date_time_value:
|
|
116
|
-
# date_to_check = plv_instance.date_time_value.date()
|
|
117
|
-
# elif hasattr(plv_instance, 'date') and plv_instance.date: # If it had a simple date field
|
|
118
|
-
# date_to_check = plv_instance.date
|
|
119
|
-
#
|
|
120
|
-
# if _is_date_in_timeframe(date_to_check, requirement):
|
|
121
|
-
# return True
|
|
122
|
-
|
|
123
|
-
# If the code reaches here, no matching model within the timeframe was found
|
|
124
|
-
# for any of the categories specified in requirement_links.
|
|
125
|
-
return False
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
def _evaluate_models_match_all(
|
|
129
|
-
requirement_links: "RequirementLinks",
|
|
130
|
-
input_links: "RequirementLinks",
|
|
131
|
-
**kwargs
|
|
132
|
-
) -> bool:
|
|
133
|
-
"""
|
|
134
|
-
Evaluates if all active links in requirement_links are present in input_links.
|
|
135
|
-
|
|
136
|
-
For each category of links in requirement_links (e.g., diseases, examinations),
|
|
137
|
-
all items specified in that category in requirement_links must be present in the
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corresponding category in input_links.
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Args:
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requirement_links: The RequirementLinks object from the Requirement model.
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input_links: The aggregated RequirementLinks object from the input arguments.
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**kwargs: Additional keyword arguments (currently unused).
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Returns:
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True if all specified items in requirement_links are found in input_links,
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False otherwise.
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"""
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active_req_links = requirement_links.active() # Get dict of non-empty lists from requirement
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if not active_req_links: # If the requirement specifies no actual items to link
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return True # Vacuously true, as there are no conditions to fail
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for link_category_name, req_items_list in active_req_links.items():
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input_items_list = getattr(input_links, link_category_name, [])
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try:
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set_input_items = set(input_items_list)
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set_req_items = set(req_items_list)
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except TypeError:
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for req_item in req_items_list:
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if req_item not in input_items_list:
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return False
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continue
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if not set_req_items.issubset(set_input_items):
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return False
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return True
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def _evaluate_age_gte(
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requirement_links: "RequirementLinks",
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input_links: "RequirementLinks",
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requirement: "Requirement",
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**kwargs
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) -> bool:
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"""
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Checks if any patient in the input has an age greater than or equal to the requirement's numeric_value.
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Args:
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requirement_links: The RequirementLinks object from the Requirement model (not used for age checks).
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input_links: The aggregated RequirementLinks object from the input arguments.
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requirement: The Requirement instance containing the minimum age in numeric_value.
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**kwargs: Additional keyword arguments, should contain 'original_input_args' with the original Patient instances.
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|
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Returns:
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True if any patient in the input has an age >= requirement.numeric_value, False otherwise.
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"""
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|
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from endoreg_db.models.administration.person.patient import Patient
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import logging
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logger = logging.getLogger(__name__)
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|
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if requirement.numeric_value is None:
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logger.debug("age_gte: requirement.numeric_value is None, returning False")
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|
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return False # Cannot evaluate without a minimum age requirement
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198
|
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min_age = requirement.numeric_value
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logger.debug(f"age_gte: Checking if any patient has age >= {min_age}")
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|
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# Check if we have Patient instances in the original_input_args
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|
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original_args = kwargs.get('original_input_args', [])
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logger.debug(f"age_gte: Found {len(original_args)} original input arguments: {[type(arg).__name__ for arg in original_args]}")
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for i, arg in enumerate(original_args):
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logger.debug(f"age_gte: Checking argument {i}: {type(arg).__name__}")
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if isinstance(arg, Patient):
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patient_age = arg.age()
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logger.debug(f"age_gte: Patient {arg} has age {patient_age}, comparing with min_age {min_age}")
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|
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if patient_age is not None and patient_age >= min_age:
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logger.debug(f"age_gte: Patient age {patient_age} >= {min_age}, returning True")
|
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-
return True
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|
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else:
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logger.debug(f"age_gte: Patient age {patient_age} < {min_age} or is None")
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|
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# Handle QuerySets of patients
|
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216
|
-
elif hasattr(arg, 'model') and issubclass(arg.model, Patient):
|
|
217
|
-
logger.debug(f"age_gte: Found Patient QuerySet with {arg.count()} patients")
|
|
218
|
-
for patient in arg:
|
|
219
|
-
patient_age = patient.age()
|
|
220
|
-
logger.debug(f"age_gte: Patient {patient} has age {patient_age}, comparing with min_age {min_age}")
|
|
221
|
-
if patient_age is not None and patient_age >= min_age:
|
|
222
|
-
logger.debug(f"age_gte: Patient age {patient_age} >= {min_age}, returning True")
|
|
223
|
-
return True
|
|
224
|
-
else:
|
|
225
|
-
logger.debug(f"age_gte: Argument {i} is not a Patient or Patient QuerySet: {type(arg)}")
|
|
226
|
-
|
|
227
|
-
logger.debug(f"age_gte: No patient found with age >= {min_age}, returning False")
|
|
228
|
-
return False
|
|
229
|
-
|
|
230
|
-
|
|
231
|
-
def _evaluate_age_lte(
|
|
232
|
-
requirement_links: "RequirementLinks",
|
|
233
|
-
input_links: "RequirementLinks",
|
|
234
|
-
requirement: "Requirement",
|
|
235
|
-
**kwargs
|
|
236
|
-
) -> bool:
|
|
237
|
-
"""
|
|
238
|
-
Checks if any patient in the input has an age less than or equal to the requirement's numeric_value.
|
|
239
|
-
|
|
240
|
-
Args:
|
|
241
|
-
requirement_links: The RequirementLinks object from the Requirement model (not used for age checks).
|
|
242
|
-
input_links: The aggregated RequirementLinks object from the input arguments.
|
|
243
|
-
requirement: The Requirement instance containing the maximum age in numeric_value.
|
|
244
|
-
**kwargs: Additional keyword arguments, should contain 'original_input_args' with the original Patient instances.
|
|
245
|
-
|
|
246
|
-
Returns:
|
|
247
|
-
True if any patient in the input has an age <= requirement.numeric_value, False otherwise.
|
|
248
|
-
"""
|
|
249
|
-
from endoreg_db.models.administration.person.patient import Patient
|
|
250
|
-
|
|
251
|
-
if requirement.numeric_value is None:
|
|
252
|
-
return False # Cannot evaluate without a maximum age requirement
|
|
253
|
-
|
|
254
|
-
max_age = requirement.numeric_value
|
|
255
|
-
|
|
256
|
-
# Check if we have Patient instances in the original_input_args
|
|
257
|
-
original_args = kwargs.get('original_input_args', [])
|
|
258
|
-
for arg in original_args:
|
|
259
|
-
if isinstance(arg, Patient):
|
|
260
|
-
patient_age = arg.age()
|
|
261
|
-
if patient_age is not None and patient_age <= max_age:
|
|
262
|
-
return True
|
|
263
|
-
# Handle QuerySets of patients
|
|
264
|
-
elif hasattr(arg, 'model') and issubclass(arg.model, Patient):
|
|
265
|
-
for patient in arg:
|
|
266
|
-
patient_age = patient.age()
|
|
267
|
-
if patient_age is not None and patient_age <= max_age:
|
|
268
|
-
return True
|
|
269
|
-
|
|
270
|
-
return False
|
|
271
|
-
|
|
272
|
-
|
|
273
|
-
def dispatch_operator_evaluation(
|
|
274
|
-
operator_name: str,
|
|
275
|
-
requirement_links: "RequirementLinks",
|
|
276
|
-
input_links: "RequirementLinks",
|
|
277
|
-
**kwargs
|
|
278
|
-
) -> bool:
|
|
279
|
-
"""
|
|
280
|
-
Dispatches the evaluation to the appropriate function based on the operator name.
|
|
281
|
-
|
|
282
|
-
Args:
|
|
283
|
-
operator_name: The name of the operator to evaluate.
|
|
284
|
-
requirement_links: The RequirementLinks object from the Requirement model.
|
|
285
|
-
input_links: The aggregated RequirementLinks object from the input arguments.
|
|
286
|
-
**kwargs: Additional keyword arguments for specific operator logic.
|
|
287
|
-
For lab value operators, this includes 'requirement' (the Requirement model instance).
|
|
288
|
-
|
|
289
|
-
Returns:
|
|
290
|
-
True if the condition defined by the operator is met, False otherwise.
|
|
291
|
-
|
|
292
|
-
Raises:
|
|
293
|
-
NotImplementedError: If the evaluation logic for the operator's name is not implemented.
|
|
294
|
-
"""
|
|
295
|
-
from .lab_value_operators import LAB_VALUE_OPERATOR_FUNCTIONS
|
|
296
|
-
from endoreg_db.models.requirement.requirement import Requirement # Runtime import for isinstance
|
|
297
|
-
|
|
298
|
-
eval_func = None
|
|
299
|
-
requirement = kwargs.get("requirement") # Get requirement for operators that need it
|
|
300
|
-
|
|
301
|
-
if operator_name == "models_match_any":
|
|
302
|
-
eval_func = _evaluate_models_match_any
|
|
303
|
-
return eval_func(
|
|
304
|
-
requirement_links=requirement_links,
|
|
305
|
-
input_links=input_links,
|
|
306
|
-
**kwargs
|
|
307
|
-
)
|
|
308
|
-
elif operator_name == "models_match_all":
|
|
309
|
-
eval_func = _evaluate_models_match_all
|
|
310
|
-
return eval_func(
|
|
311
|
-
requirement_links=requirement_links,
|
|
312
|
-
input_links=input_links,
|
|
313
|
-
**kwargs
|
|
314
|
-
)
|
|
315
|
-
elif operator_name == "models_match_any_in_timeframe":
|
|
316
|
-
# 'requirement' is already extracted from kwargs via requirement = kwargs.get("requirement")
|
|
317
|
-
if not isinstance(requirement, Requirement): # Ensure requirement is present and correct type
|
|
318
|
-
raise ValueError("models_match_any_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
|
|
319
|
-
|
|
320
|
-
# Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice,
|
|
321
|
-
# as it's already an explicit parameter for _evaluate_models_match_any_in_timeframe.
|
|
322
|
-
kwargs_for_eval = {k: v for k, v in kwargs.items() if k != 'requirement'}
|
|
323
|
-
|
|
324
|
-
eval_func = _evaluate_models_match_any_in_timeframe
|
|
325
|
-
return eval_func(
|
|
326
|
-
requirement_links=requirement_links,
|
|
327
|
-
input_links=input_links,
|
|
328
|
-
requirement=requirement, # Pass the requirement instance explicitly
|
|
329
|
-
**kwargs_for_eval # Pass the remaining kwargs
|
|
330
|
-
)
|
|
331
|
-
elif operator_name in LAB_VALUE_OPERATOR_FUNCTIONS:
|
|
332
|
-
if not isinstance(requirement, Requirement): # Ensure requirement is present and correct type
|
|
333
|
-
raise ValueError(f"Lab value operator \'{operator_name}\' requires a valid 'requirement' instance in kwargs.")
|
|
334
|
-
|
|
335
|
-
eval_func = LAB_VALUE_OPERATOR_FUNCTIONS[operator_name]
|
|
336
|
-
return eval_func(
|
|
337
|
-
input_links=input_links,
|
|
338
|
-
requirement=requirement,
|
|
339
|
-
operator_kwargs=kwargs
|
|
340
|
-
)
|
|
341
|
-
elif operator_name == "age_gte":
|
|
342
|
-
if not isinstance(requirement, Requirement):
|
|
343
|
-
raise ValueError("age_gte operator requires a valid 'requirement' instance in kwargs.")
|
|
344
|
-
|
|
345
|
-
# Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice
|
|
346
|
-
kwargs_for_eval = {k: v for k, v in kwargs.items() if k != 'requirement'}
|
|
347
|
-
|
|
348
|
-
return _evaluate_age_gte(
|
|
349
|
-
requirement_links=requirement_links,
|
|
350
|
-
input_links=input_links,
|
|
351
|
-
requirement=requirement,
|
|
352
|
-
**kwargs_for_eval
|
|
353
|
-
)
|
|
354
|
-
elif operator_name == "age_lte":
|
|
355
|
-
if not isinstance(requirement, Requirement):
|
|
356
|
-
raise ValueError("age_lte operator requires a valid 'requirement' instance in kwargs.")
|
|
357
|
-
|
|
358
|
-
# Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice
|
|
359
|
-
kwargs_for_eval = {k: v for k, v in kwargs.items() if k != 'requirement'}
|
|
360
|
-
|
|
361
|
-
return _evaluate_age_lte(
|
|
362
|
-
requirement_links=requirement_links,
|
|
363
|
-
input_links=input_links,
|
|
364
|
-
requirement=requirement,
|
|
365
|
-
**kwargs_for_eval
|
|
366
|
-
)
|
|
367
|
-
else:
|
|
368
|
-
raise NotImplementedError(f"Evaluation logic for operator '{operator_name}' is not implemented.")
|