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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from django.core.management.base import BaseCommand
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from endoreg_db.models import (
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Finding, FindingType, Examination,
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FindingClassification, FindingClassificationType, FindingClassificationChoice,
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Organ,
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FindingIntervention, FindingInterventionType, LabValue, Contraindication
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from endoreg_db.models import (
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Finding,
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FindingClassification,
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FindingClassificationChoice,
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FindingClassificationType,
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FindingIntervention,
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FindingInterventionType,
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FindingType,
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from ...data import (
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FINDING_CLASSIFICATION_CHOICE_DATA_DIR,
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FINDING_CLASSIFICATION_DATA_DIR,
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FINDING_CLASSIFICATION_TYPE_DATA_DIR,
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FINDING_DATA_DIR,
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FINDING_INTERVETION_DATA_DIR,
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FINDING_TYPE_DATA_DIR,
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FINIDNG_INTERVENTION_TYPE_DATA_DIR,
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FINDING_CLASSIFICATION_TYPE_DATA_DIR,
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FINDING_CLASSIFICATION_DATA_DIR,
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FINDING_CLASSIFICATION_CHOICE_DATA_DIR
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)
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FindingIntervention.__name__,
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FindingType.__name__,
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Finding.__name__,
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FindingClassificationType.__name__,
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FindingClassificationChoice.__name__,
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FindingClassificationType.__name__,
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FindingClassification.__name__,
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Finding.__name__,
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], # e.g. ["intervention_types"]
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"foreign_key_models": [
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FindingType,
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Examination,
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FindingIntervention,
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FindingIntervention,
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FindingIntervention,
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] # e.g. [InterventionType]
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"dir": FINDING_DATA_DIR,
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"model": Finding,
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"foreign_keys": ["finding_types", "finding_interventions", "finding_classifications", "caused_by_interventions"],
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"foreign_key_models": [FindingType, FindingIntervention, FindingClassification, FindingIntervention],
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"model": FindingInterventionType,
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"foreign_keys": [],
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"foreign_key_models": []
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"dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR,
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"model": FindingInterventionType,
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"foreign_keys": [],
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51
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"foreign_key_models": [],
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FindingIntervention.__name__: {
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"dir": FINDING_INTERVETION_DATA_DIR,
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"foreign_keys": [
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"required_lab_values",
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"contraindications"
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], # e.g. ["intervention_types"]
|
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"foreign_key_models": [
|
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FindingInterventionType,
|
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LabValue,
|
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|
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Contraindication
|
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] # e.g. [InterventionType]
|
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"dir": FINDING_INTERVETION_DATA_DIR,
|
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|
+
"model": FindingIntervention,
|
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"foreign_keys": ["intervention_types"],
|
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|
+
"foreign_key_models": [FindingInterventionType],
|
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58
|
},
|
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59
|
FindingClassificationType.__name__: {
|
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|
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|
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"model": FindingClassificationType,
|
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"foreign_keys": [],
|
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"foreign_key_models": []
|
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|
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"dir": FINDING_CLASSIFICATION_TYPE_DATA_DIR,
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"model": FindingClassificationType,
|
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"foreign_keys": [],
|
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63
|
+
"foreign_key_models": [],
|
|
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64
|
},
|
|
78
65
|
FindingClassification.__name__: {
|
|
79
|
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"dir": FINDING_CLASSIFICATION_DATA_DIR,
|
|
80
|
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"model": FindingClassification,
|
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81
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"foreign_keys": [
|
|
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|
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"classification_types",
|
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|
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"findings",
|
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|
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"examinations",
|
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85
|
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"finding_types",
|
|
86
|
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"choices"
|
|
87
|
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], # e.g. ["intervention_types"]
|
|
66
|
+
"dir": FINDING_CLASSIFICATION_DATA_DIR,
|
|
67
|
+
"model": FindingClassification,
|
|
68
|
+
"foreign_keys": ["classification_types", "findings", "finding_types", "choices"],
|
|
88
69
|
"foreign_key_models": [
|
|
89
70
|
FindingClassificationType,
|
|
90
71
|
Finding,
|
|
91
|
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Examination,
|
|
92
72
|
FindingType,
|
|
93
73
|
FindingClassificationChoice,
|
|
94
|
-
]
|
|
74
|
+
],
|
|
95
75
|
},
|
|
96
76
|
FindingClassificationChoice.__name__: {
|
|
97
|
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"dir": FINDING_CLASSIFICATION_CHOICE_DATA_DIR,
|
|
98
|
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"model": FindingClassificationChoice,
|
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99
|
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"foreign_keys": [
|
|
100
|
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|
|
101
|
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], # e.g. ["intervention_types"]
|
|
102
|
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"foreign_key_models": [
|
|
103
|
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# FindingClassification
|
|
104
|
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] # e.g. [InterventionType]
|
|
77
|
+
"dir": FINDING_CLASSIFICATION_CHOICE_DATA_DIR,
|
|
78
|
+
"model": FindingClassificationChoice,
|
|
79
|
+
"foreign_keys": [],
|
|
80
|
+
"foreign_key_models": [],
|
|
105
81
|
},
|
|
106
82
|
}
|
|
107
83
|
|
|
84
|
+
|
|
108
85
|
class Command(BaseCommand):
|
|
109
86
|
help = """Load all .yaml files in the data/intervention directory
|
|
110
87
|
into the Intervention and InterventionType model"""
|
|
111
88
|
|
|
112
89
|
def add_arguments(self, parser):
|
|
113
90
|
parser.add_argument(
|
|
114
|
-
|
|
115
|
-
action=
|
|
116
|
-
help=
|
|
91
|
+
"--verbose",
|
|
92
|
+
action="store_true",
|
|
93
|
+
help="Display verbose output",
|
|
117
94
|
)
|
|
118
95
|
|
|
119
96
|
def handle(self, *args, **options):
|
|
120
|
-
verbose = options[
|
|
97
|
+
verbose = options["verbose"]
|
|
121
98
|
for model_name in IMPORT_MODELS:
|
|
122
99
|
_metadata = IMPORT_METADATA[model_name]
|
|
123
|
-
load_model_data_from_yaml(
|
|
124
|
-
self,
|
|
125
|
-
model_name,
|
|
126
|
-
_metadata,
|
|
127
|
-
verbose
|
|
128
|
-
)
|
|
100
|
+
load_model_data_from_yaml(self, model_name, _metadata, verbose)
|
|
@@ -1,51 +1,49 @@
|
|
|
1
|
-
from django.conf import settings
|
|
2
1
|
import os
|
|
2
|
+
|
|
3
|
+
from django.conf import settings
|
|
3
4
|
from django.core.management.base import BaseCommand
|
|
5
|
+
|
|
6
|
+
from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
|
|
4
7
|
from ...models import InformationSource, InformationSourceType
|
|
5
8
|
from ...utils import load_model_data_from_yaml
|
|
6
|
-
from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
|
|
7
9
|
|
|
8
|
-
SOURCE_DIR = INFORMATION_DATA_DIR
|
|
10
|
+
SOURCE_DIR = INFORMATION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
|
|
9
11
|
|
|
10
12
|
|
|
11
|
-
IMPORT_MODELS = [
|
|
13
|
+
IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
|
|
12
14
|
InformationSourceType.__name__,
|
|
13
15
|
InformationSource.__name__,
|
|
14
16
|
]
|
|
15
17
|
|
|
16
18
|
IMPORT_METADATA = {
|
|
17
19
|
InformationSourceType.__name__: {
|
|
18
|
-
"dir": INFORMATION_SOURCE_TYPE_DATA_DIR,
|
|
19
|
-
"model": InformationSourceType,
|
|
20
|
-
"foreign_keys": [],
|
|
21
|
-
"foreign_key_models": []
|
|
20
|
+
"dir": INFORMATION_SOURCE_TYPE_DATA_DIR, # e.g. "intervention_type"
|
|
21
|
+
"model": InformationSourceType,
|
|
22
|
+
"foreign_keys": [], # e.g. ["intervention_types"]
|
|
23
|
+
"foreign_key_models": [], # e.g. [InterventionType]
|
|
22
24
|
},
|
|
23
25
|
InformationSource.__name__: {
|
|
24
|
-
"dir": SOURCE_DIR,
|
|
25
|
-
"model": InformationSource,
|
|
26
|
-
"foreign_keys": ["information_source_types"],
|
|
27
|
-
"foreign_key_models": [InformationSourceType]
|
|
28
|
-
}
|
|
26
|
+
"dir": SOURCE_DIR, # e.g. "interventions"
|
|
27
|
+
"model": InformationSource,
|
|
28
|
+
"foreign_keys": ["information_source_types"], # e.g. ["intervention_types"]
|
|
29
|
+
"foreign_key_models": [InformationSourceType], # e.g. [InterventionType]
|
|
30
|
+
},
|
|
29
31
|
}
|
|
30
32
|
|
|
33
|
+
|
|
31
34
|
class Command(BaseCommand):
|
|
32
35
|
help = """Load all .yaml files in the data/intervention directory
|
|
33
36
|
into the Intervention and InterventionType model"""
|
|
34
37
|
|
|
35
38
|
def add_arguments(self, parser):
|
|
36
39
|
parser.add_argument(
|
|
37
|
-
|
|
38
|
-
action=
|
|
39
|
-
help=
|
|
40
|
+
"--verbose",
|
|
41
|
+
action="store_true",
|
|
42
|
+
help="Display verbose output",
|
|
40
43
|
)
|
|
41
44
|
|
|
42
45
|
def handle(self, *args, **options):
|
|
43
|
-
verbose = options[
|
|
46
|
+
verbose = options["verbose"]
|
|
44
47
|
for model_name in IMPORT_MODELS:
|
|
45
48
|
_metadata = IMPORT_METADATA[model_name]
|
|
46
|
-
load_model_data_from_yaml(
|
|
47
|
-
self,
|
|
48
|
-
model_name,
|
|
49
|
-
_metadata,
|
|
50
|
-
verbose
|
|
51
|
-
)
|
|
49
|
+
load_model_data_from_yaml(self, model_name, _metadata, verbose)
|
|
@@ -1,50 +1,41 @@
|
|
|
1
1
|
from django.core.management.base import BaseCommand
|
|
2
|
+
|
|
2
3
|
from endoreg_db.models import LabValue as MODEL_0
|
|
3
|
-
from endoreg_db.models import PatientLabSampleType,
|
|
4
|
-
|
|
4
|
+
from endoreg_db.models import NumericValueDistribution, PatientLabSampleType, Unit
|
|
5
|
+
|
|
5
6
|
from ...data import LAB_VALUE_DATA_DIR as SOURCE_DIR
|
|
6
7
|
from ...data import PATIENT_LAB_SAMPLE_TYPE_DATA_DIR
|
|
8
|
+
from ...utils import load_model_data_from_yaml
|
|
7
9
|
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
|
|
10
|
+
IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
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MODEL_0.__name__,
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PatientLabSampleType.__name__
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PatientLabSampleType.__name__,
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]
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IMPORT_METADATA = {
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"dir": SOURCE_DIR,
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"model": MODEL_0,
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"foreign_keys": ["default_unit","default_numerical_value_distribution"],
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"foreign_key_models": [Unit, NumericValueDistribution]
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"dir": SOURCE_DIR, # e.g. "interventions"
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"model": MODEL_0,
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"foreign_keys": ["default_unit", "default_numerical_value_distribution"], # e.g. ["intervention_types"]
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"foreign_key_models": [Unit, NumericValueDistribution], # e.g. [InterventionType]
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},
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PatientLabSampleType.__name__: {
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"dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR,
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"model": PatientLabSampleType,
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"foreign_keys": [],
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"foreign_key_models": []
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}
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PatientLabSampleType.__name__: {"dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR, "model": PatientLabSampleType, "foreign_keys": [], "foreign_key_models": []},
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}
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class Command(BaseCommand):
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help = """Load all .yaml files in the data/intervention directory
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into the Intervention and InterventionType model"""
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def add_arguments(self, parser):
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parser.add_argument(
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action=
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help=
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"--verbose",
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action="store_true",
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help="Display verbose output",
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)
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def handle(self, *args, **options):
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verbose = options[
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+
verbose = options["verbose"]
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for model_name in IMPORT_MODELS:
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_metadata = IMPORT_METADATA[model_name]
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-
load_model_data_from_yaml(
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-
self,
|
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model_name,
|
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-
_metadata,
|
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-
verbose
|
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-
)
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load_model_data_from_yaml(self, model_name, _metadata, verbose)
|
|
@@ -1,25 +1,26 @@
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1
1
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from django.core.management.base import BaseCommand
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2
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+
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2
3
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from endoreg_db.models import (
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4
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Disease,
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5
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DiseaseClassificationChoice,
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6
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Event,
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7
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+
InformationSource,
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3
8
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Medication,
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4
9
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MedicationIndication,
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5
10
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MedicationIndicationType,
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6
11
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MedicationIntakeTime,
|
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7
12
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MedicationSchedule,
|
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8
13
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Unit,
|
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9
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-
Disease,
|
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10
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-
Event,
|
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11
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-
InformationSource,
|
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12
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DiseaseClassificationChoice,
|
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13
14
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)
|
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14
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-
|
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15
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+
|
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15
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|
from ...data import (
|
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16
17
|
MEDICATION_DATA_DIR,
|
|
18
|
+
MEDICATION_INDICATION_DATA_DIR,
|
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17
19
|
MEDICATION_INDICATION_TYPE_DATA_DIR,
|
|
18
20
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MEDICATION_INTAKE_TIME_DATA_DIR,
|
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19
21
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MEDICATION_SCHEDULE_DATA_DIR,
|
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20
|
-
MEDICATION_INDICATION_DATA_DIR,
|
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21
22
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)
|
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-
|
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23
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+
from ...utils import load_model_data_from_yaml
|
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23
24
|
|
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24
25
|
IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
|
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25
26
|
Medication.__name__,
|
|
@@ -32,25 +33,25 @@ IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
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32
33
|
IMPORT_METADATA = {
|
|
33
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Medication.__name__: {
|
|
34
35
|
"dir": MEDICATION_DATA_DIR, # e.g. "interventions"
|
|
35
|
-
"model": Medication,
|
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36
|
+
"model": Medication,
|
|
36
37
|
"foreign_keys": ["default_unit"], # e.g. ["intervention_types"]
|
|
37
38
|
"foreign_key_models": [Unit], # e.g. [InterventionType]
|
|
38
39
|
},
|
|
39
40
|
MedicationIndicationType.__name__: {
|
|
40
41
|
"dir": MEDICATION_INDICATION_TYPE_DATA_DIR, # e.g. "interventions"
|
|
41
|
-
"model": MedicationIndicationType,
|
|
42
|
+
"model": MedicationIndicationType,
|
|
42
43
|
"foreign_keys": [], # e.g. ["intervention_types"]
|
|
43
44
|
"foreign_key_models": [], # e.g. [InterventionType]
|
|
44
45
|
},
|
|
45
46
|
MedicationIntakeTime.__name__: {
|
|
46
47
|
"dir": MEDICATION_INTAKE_TIME_DATA_DIR, # e.g. "interventions"
|
|
47
|
-
"model": MedicationIntakeTime,
|
|
48
|
+
"model": MedicationIntakeTime,
|
|
48
49
|
"foreign_keys": [], # e.g. ["intervention_types"]
|
|
49
50
|
"foreign_key_models": [], # e.g. [InterventionType]
|
|
50
51
|
},
|
|
51
52
|
MedicationSchedule.__name__: {
|
|
52
53
|
"dir": MEDICATION_SCHEDULE_DATA_DIR, # e.g. "interventions"
|
|
53
|
-
"model": MedicationSchedule,
|
|
54
|
+
"model": MedicationSchedule,
|
|
54
55
|
"foreign_keys": [
|
|
55
56
|
"medication",
|
|
56
57
|
"intake_times",
|
|
@@ -64,7 +65,7 @@ IMPORT_METADATA = {
|
|
|
64
65
|
},
|
|
65
66
|
MedicationIndication.__name__: {
|
|
66
67
|
"dir": MEDICATION_INDICATION_DATA_DIR, # e.g. "interventions"
|
|
67
|
-
"model": MedicationIndication,
|
|
68
|
+
"model": MedicationIndication,
|
|
68
69
|
"foreign_keys": [
|
|
69
70
|
"indication_type",
|
|
70
71
|
"medication_schedules",
|
|
@@ -1,43 +1,39 @@
|
|
|
1
1
|
from django.core.management.base import BaseCommand
|
|
2
|
+
|
|
2
3
|
from endoreg_db.models import Organ
|
|
4
|
+
|
|
5
|
+
from ...data import ORGAN_DATA_DIR
|
|
3
6
|
from ...utils import load_model_data_from_yaml
|
|
4
|
-
from ...data import (
|
|
5
|
-
ORGAN_DATA_DIR
|
|
6
|
-
)
|
|
7
7
|
|
|
8
8
|
MODEL_0 = Organ
|
|
9
9
|
|
|
10
|
-
IMPORT_MODELS = [
|
|
11
|
-
MODEL_0.__name__
|
|
10
|
+
IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
|
|
11
|
+
MODEL_0.__name__, #
|
|
12
12
|
]
|
|
13
13
|
|
|
14
14
|
IMPORT_METADATA = {
|
|
15
15
|
MODEL_0.__name__: {
|
|
16
|
-
"dir": ORGAN_DATA_DIR,
|
|
17
|
-
"model": MODEL_0,
|
|
18
|
-
"foreign_keys": [],
|
|
19
|
-
"foreign_key_models": []
|
|
16
|
+
"dir": ORGAN_DATA_DIR, # e.g. "interventions"
|
|
17
|
+
"model": MODEL_0,
|
|
18
|
+
"foreign_keys": [], # e.g. ["intervention_types"]
|
|
19
|
+
"foreign_key_models": [], # e.g. [InterventionType]
|
|
20
20
|
}
|
|
21
21
|
}
|
|
22
22
|
|
|
23
|
+
|
|
23
24
|
class Command(BaseCommand):
|
|
24
25
|
help = """Load all .yaml files in the data/intervention directory
|
|
25
26
|
into the Intervention and InterventionType model"""
|
|
26
27
|
|
|
27
28
|
def add_arguments(self, parser):
|
|
28
29
|
parser.add_argument(
|
|
29
|
-
|
|
30
|
-
action=
|
|
31
|
-
help=
|
|
30
|
+
"--verbose",
|
|
31
|
+
action="store_true",
|
|
32
|
+
help="Display verbose output",
|
|
32
33
|
)
|
|
33
34
|
|
|
34
35
|
def handle(self, *args, **options):
|
|
35
|
-
verbose = options[
|
|
36
|
+
verbose = options["verbose"]
|
|
36
37
|
for model_name in IMPORT_MODELS:
|
|
37
38
|
_metadata = IMPORT_METADATA[model_name]
|
|
38
|
-
load_model_data_from_yaml(
|
|
39
|
-
self,
|
|
40
|
-
model_name,
|
|
41
|
-
_metadata,
|
|
42
|
-
verbose
|
|
43
|
-
)
|
|
39
|
+
load_model_data_from_yaml(self, model_name, _metadata, verbose)
|