PyPI - endoreg-db - Versions diffs - 0.3.6__py3-none-any.whl → 0.8.6.1__py3-none-any.whl - Mend

endoreg-db 0.3.6py3-none-any.whl → 0.8.6.1py3-none-any.whl

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endoreg_db/admin.py +92 -3
endoreg_db/api_urls.py +4 -0
endoreg_db/apps.py +18 -6
endoreg_db/assets/dummy_model.ckpt +1 -0
endoreg_db/codemods/readme.md +88 -0
endoreg_db/codemods/rename_datetime_fields.py +92 -0
endoreg_db/config/env.py +101 -0
endoreg_db/data/__init__.py +144 -65
endoreg_db/data/ai_model/data.yaml +7 -0
endoreg_db/data/{label → ai_model_label}/label/data.yaml +88 -62
endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
endoreg_db/data/{label → ai_model_label}/label-type/data.yaml +6 -6
endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
endoreg_db/data/{model_type → ai_model_type}/data.yaml +6 -6
endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -167
endoreg_db/data/case_template/rule/01_patient-set-age.yaml +7 -7
endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +8 -8
endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +22 -22
endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +18 -18
endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +18 -18
endoreg_db/data/case_template/rule/19_create_patient.yaml +16 -16
endoreg_db/data/case_template/rule_type/base_types.yaml +35 -35
endoreg_db/data/case_template/rule_value_type/base_types.yaml +58 -58
endoreg_db/data/case_template/template/base.yaml +7 -7
endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +2 -2
endoreg_db/data/case_template/tmp/_rule_value +13 -13
endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -21
endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +9 -9
endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +6 -6
endoreg_db/data/center/data.yaml +90 -59
endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -144
endoreg_db/data/center_shift/ukw.yaml +9 -0
endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -48
endoreg_db/data/contraindication/bleeding.yaml +11 -0
endoreg_db/data/db_summary.csv +58 -0
endoreg_db/data/db_summary.xlsx +0 -0
endoreg_db/data/disease/cardiovascular.yaml +37 -37
endoreg_db/data/disease/hepatology.yaml +4 -4
endoreg_db/data/disease/misc.yaml +5 -6
endoreg_db/data/disease/renal.yaml +4 -4
endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -6
endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +5 -5
endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -41
endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +19 -19
endoreg_db/data/distribution/date/patient.yaml +6 -6
endoreg_db/data/distribution/numeric/data.yaml +14 -0
endoreg_db/data/distribution/single_categorical/patient.yaml +6 -6
endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -132
endoreg_db/data/endoscope/data.yaml +93 -0
endoreg_db/data/endoscope_type/data.yaml +10 -10
endoreg_db/data/endoscopy_processor/data.yaml +50 -45
endoreg_db/data/event/cardiology.yaml +15 -28
endoreg_db/data/event/neurology.yaml +13 -13
endoreg_db/data/event/surgery.yaml +12 -12
endoreg_db/data/event/thrombembolism.yaml +19 -19
endoreg_db/data/examination/examinations/data.yaml +72 -66
endoreg_db/data/examination/time/data.yaml +47 -47
endoreg_db/data/examination/time-type/data.yaml +7 -7
endoreg_db/data/examination/type/data.yaml +17 -5
endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
endoreg_db/data/finding/anatomy_colon.yaml +128 -0
endoreg_db/data/finding/colonoscopy.yaml +40 -0
endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
endoreg_db/data/finding/complication.yaml +16 -0
endoreg_db/data/finding/data.yaml +105 -0
endoreg_db/data/finding/examination_setting.yaml +16 -0
endoreg_db/data/finding/medication_related.yaml +18 -0
endoreg_db/data/finding/outcome.yaml +12 -0
endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
endoreg_db/data/finding_classification/medication_related.yaml +23 -0
endoreg_db/data/finding_classification/visualized.yaml +33 -0
endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
endoreg_db/data/finding_type/data.yaml +43 -0
endoreg_db/data/gender/data.yaml +42 -18
endoreg_db/data/information_source/annotation.yaml +6 -0
endoreg_db/data/information_source/data.yaml +30 -30
endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
endoreg_db/data/information_source/medication.yaml +5 -5
endoreg_db/data/information_source/prediction.yaml +7 -0
endoreg_db/data/information_source_type/data.yaml +8 -0
endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -31
endoreg_db/data/lab_value/coagulation.yaml +54 -49
endoreg_db/data/lab_value/electrolytes.yaml +228 -190
endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -121
endoreg_db/data/lab_value/hematology.yaml +184 -169
endoreg_db/data/lab_value/hormones.yaml +59 -53
endoreg_db/data/lab_value/lipids.yaml +53 -44
endoreg_db/data/lab_value/misc.yaml +76 -30
endoreg_db/data/lab_value/renal_function.yaml +12 -11
endoreg_db/data/log_type/data.yaml +57 -0
endoreg_db/data/lx_client_tag/base.yaml +54 -0
endoreg_db/data/lx_client_type/base.yaml +30 -0
endoreg_db/data/lx_permission/base.yaml +24 -0
endoreg_db/data/lx_permission/endoreg.yaml +52 -0
endoreg_db/data/medication/anticoagulation.yaml +64 -64
endoreg_db/data/medication/tah.yaml +69 -69
endoreg_db/data/medication_indication/anticoagulation.yaml +115 -120
endoreg_db/data/medication_indication_type/data.yaml +10 -10
endoreg_db/data/medication_indication_type/thrombembolism.yaml +40 -40
endoreg_db/data/medication_intake_time/base.yaml +30 -30
endoreg_db/data/medication_schedule/apixaban.yaml +94 -94
endoreg_db/data/medication_schedule/ass.yaml +12 -12
endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -26
endoreg_db/data/names_first/first_names.yaml +54 -0
endoreg_db/data/names_last/last_names.yaml +51 -0
endoreg_db/data/network_device/data.yaml +59 -0
endoreg_db/data/network_device_type/data.yaml +12 -0
endoreg_db/data/organ/data.yaml +29 -0
endoreg_db/data/patient_lab_sample_type/generic.yaml +5 -5
endoreg_db/data/pdf_type/data.yaml +46 -28
endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
endoreg_db/data/profession/data.yaml +70 -70
endoreg_db/data/qualification/endoscopy.yaml +36 -0
endoreg_db/data/qualification/m2.yaml +39 -0
endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
endoreg_db/data/qualification/sonography.yaml +36 -0
endoreg_db/data/qualification_type/base.yaml +29 -0
endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -55
endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -26
endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -19
endoreg_db/data/requirement/age.yaml +26 -0
endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
endoreg_db/data/requirement/disease_misc.yaml +12 -0
endoreg_db/data/requirement/disease_renal.yaml +96 -0
endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
endoreg_db/data/requirement/event_cardiology.yaml +251 -0
endoreg_db/data/requirement/event_requirements.yaml +145 -0
endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
endoreg_db/data/requirement/gender.yaml +25 -0
endoreg_db/data/requirement/lab_value.yaml +441 -0
endoreg_db/data/requirement/medication.yaml +93 -0
endoreg_db/data/requirement_operator/age.yaml +13 -0
endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
endoreg_db/data/requirement_set_type/data.yaml +20 -0
endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
endoreg_db/data/risk/bleeding.yaml +26 -0
endoreg_db/data/risk/thrombosis.yaml +37 -0
endoreg_db/data/risk_type/data.yaml +27 -0
endoreg_db/data/setup_config.yaml +38 -0
endoreg_db/data/shift/endoscopy.yaml +21 -0
endoreg_db/data/shift/m2.yaml +0 -0
endoreg_db/data/shift_type/base.yaml +35 -0
endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
endoreg_db/data/unit/concentration.yaml +115 -92
endoreg_db/data/unit/data.yaml +17 -17
endoreg_db/data/unit/length.yaml +30 -30
endoreg_db/data/unit/misc.yaml +19 -19
endoreg_db/data/unit/rate.yaml +5 -5
endoreg_db/data/unit/time.yaml +48 -13
endoreg_db/data/unit/volume.yaml +35 -35
endoreg_db/data/unit/weight.yaml +37 -37
endoreg_db/data/waste/data.yaml +11 -11
endoreg_db/exceptions.py +19 -0
endoreg_db/factories/__init__.py +0 -0
endoreg_db/forms/__init__.py +5 -3
endoreg_db/forms/examination_form.py +11 -0
endoreg_db/forms/patient_finding_intervention_form.py +18 -0
endoreg_db/forms/patient_form.py +27 -0
endoreg_db/forms/questionnaires/__init__.py +1 -1
endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
endoreg_db/forms/settings/__init__.py +8 -8
endoreg_db/forms/unit.py +5 -5
endoreg_db/helpers/__init__.py +0 -0
endoreg_db/helpers/count_db.py +45 -0
endoreg_db/helpers/data_loader.py +208 -0
endoreg_db/helpers/default_objects.py +378 -0
endoreg_db/helpers/download_segmentation_model.py +31 -0
endoreg_db/helpers/interact.py +6 -0
endoreg_db/helpers/test_video_helper.py +119 -0
endoreg_db/logger_conf.py +140 -0
endoreg_db/management/__init__.py +1 -0
endoreg_db/management/commands/__init__.py +1 -0
endoreg_db/management/commands/anonymize_video.py +0 -0
endoreg_db/management/commands/check_auth.py +125 -0
endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
endoreg_db/management/commands/fix_video_paths.py +165 -0
endoreg_db/management/commands/import_fallback_video.py +203 -0
endoreg_db/management/commands/import_report.py +298 -0
endoreg_db/management/commands/import_video.py +423 -0
endoreg_db/management/commands/import_video_with_classification.py +367 -0
endoreg_db/management/commands/init_default_ai_model.py +112 -0
endoreg_db/management/commands/load_ai_model_data.py +77 -45
endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
endoreg_db/management/commands/load_base_db_data.py +192 -128
endoreg_db/management/commands/load_center_data.py +68 -43
endoreg_db/management/commands/{load_medication_intake_time_data.py → load_contraindication_data.py} +40 -40
endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
endoreg_db/management/commands/load_disease_classification_data.py +40 -40
endoreg_db/management/commands/load_disease_data.py +61 -39
endoreg_db/management/commands/load_distribution_data.py +65 -65
endoreg_db/management/commands/{load_endoscope_type_data.py → load_endoscope_data.py} +67 -44
endoreg_db/management/commands/load_event_data.py +40 -40
endoreg_db/management/commands/load_examination_data.py +74 -74
endoreg_db/management/commands/load_examination_indication_data.py +86 -0
endoreg_db/management/commands/load_finding_data.py +128 -0
endoreg_db/management/commands/load_gender_data.py +43 -43
endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +131 -132
endoreg_db/management/commands/load_information_source.py +50 -44
endoreg_db/management/commands/load_lab_value_data.py +49 -49
endoreg_db/management/commands/load_medication_data.py +103 -41
endoreg_db/management/commands/load_name_data.py +37 -0
endoreg_db/management/commands/{load_medication_indication_type_data.py → load_organ_data.py} +42 -40
endoreg_db/management/commands/load_pdf_type_data.py +60 -60
endoreg_db/management/commands/load_profession_data.py +43 -43
endoreg_db/management/commands/load_qualification_data.py +59 -0
endoreg_db/management/commands/{load_report_reader_flag.py → load_report_reader_flag_data.py} +45 -45
endoreg_db/management/commands/load_requirement_data.py +180 -0
endoreg_db/management/commands/load_risk_data.py +56 -0
endoreg_db/management/commands/load_shift_data.py +60 -0
endoreg_db/management/commands/load_tag_data.py +57 -0
endoreg_db/management/commands/load_unit_data.py +45 -45
endoreg_db/management/commands/load_user_groups.py +28 -28
endoreg_db/management/commands/register_ai_model.py +64 -65
endoreg_db/management/commands/reset_celery_schedule.py +9 -9
endoreg_db/management/commands/setup_endoreg_db.py +381 -0
endoreg_db/management/commands/start_filewatcher.py +106 -0
endoreg_db/management/commands/storage_management.py +548 -0
endoreg_db/management/commands/summarize_db_content.py +189 -0
endoreg_db/management/commands/validate_video.py +204 -0
endoreg_db/management/commands/validate_video_files.py +161 -0
endoreg_db/management/commands/video_validation.py +22 -0
endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
endoreg_db/mermaid/binary_classification_annotation.md +50 -0
endoreg_db/mermaid/classification.md +8 -0
endoreg_db/mermaid/examination.md +8 -0
endoreg_db/mermaid/findings.md +7 -0
endoreg_db/mermaid/image_classification.md +28 -0
endoreg_db/mermaid/interventions.md +8 -0
endoreg_db/mermaid/morphology.md +8 -0
endoreg_db/mermaid/patient_creation.md +14 -0
endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
endoreg_db/migrations/0001_initial.py +1857 -582
endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
endoreg_db/migrations/0003_add_center_display_name.py +30 -0
endoreg_db/models/__init__.py +359 -74
endoreg_db/models/administration/__init__.py +116 -0
endoreg_db/models/administration/ai/__init__.py +9 -0
endoreg_db/models/administration/ai/active_model.py +35 -0
endoreg_db/models/administration/ai/ai_model.py +156 -0
endoreg_db/models/{ai_model → administration/ai}/model_type.py +41 -26
endoreg_db/models/administration/case/__init__.py +19 -0
endoreg_db/models/administration/case/case.py +114 -0
endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +15 -6
endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +125 -81
endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +269 -276
endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +86 -73
endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +26 -28
endoreg_db/models/{center → administration/center}/__init__.py +13 -4
endoreg_db/models/administration/center/center.py +67 -0
endoreg_db/models/administration/center/center_product.py +64 -0
endoreg_db/models/administration/center/center_resource.py +49 -0
endoreg_db/models/administration/center/center_shift.py +88 -0
endoreg_db/models/administration/center/center_waste.py +30 -0
endoreg_db/models/administration/permissions/__init__.py +44 -0
endoreg_db/models/administration/person/__init__.py +24 -0
endoreg_db/models/administration/person/employee/__init__.py +3 -0
endoreg_db/models/administration/person/employee/employee.py +35 -0
endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
endoreg_db/models/administration/person/employee/employee_type.py +42 -0
endoreg_db/models/administration/person/examiner/__init__.py +4 -0
endoreg_db/models/administration/person/examiner/examiner.py +54 -0
endoreg_db/models/administration/person/names/__init__.py +0 -0
endoreg_db/models/{persons → administration/person/names}/first_name.py +18 -18
endoreg_db/models/{persons → administration/person/names}/last_name.py +18 -19
endoreg_db/models/administration/person/patient/__init__.py +5 -0
endoreg_db/models/administration/person/patient/patient.py +460 -0
endoreg_db/models/{persons → administration/person}/person.py +31 -31
endoreg_db/models/administration/person/profession/__init__.py +24 -0
endoreg_db/models/administration/person/user/__init__.py +5 -0
endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
endoreg_db/models/administration/product/__init__.py +14 -0
endoreg_db/models/administration/product/product.py +97 -0
endoreg_db/models/administration/product/product_group.py +39 -0
endoreg_db/models/administration/product/product_material.py +54 -0
endoreg_db/models/{product → administration/product}/product_weight.py +47 -26
endoreg_db/models/{product → administration/product}/reference_product.py +130 -99
endoreg_db/models/administration/qualification/__init__.py +7 -0
endoreg_db/models/administration/qualification/qualification.py +37 -0
endoreg_db/models/administration/qualification/qualification_type.py +35 -0
endoreg_db/models/administration/shift/__init__.py +9 -0
endoreg_db/models/administration/shift/scheduled_days.py +69 -0
endoreg_db/models/administration/shift/shift.py +51 -0
endoreg_db/models/administration/shift/shift_type.py +108 -0
endoreg_db/models/label/__init__.py +24 -1
endoreg_db/models/label/annotation/__init__.py +12 -0
endoreg_db/models/label/annotation/image_classification.py +84 -0
endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
endoreg_db/models/label/label.py +83 -84
endoreg_db/models/label/label_set.py +53 -0
endoreg_db/models/label/label_type.py +29 -0
endoreg_db/models/label/label_video_segment/__init__.py +3 -0
endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
endoreg_db/models/label/video_segmentation_label.py +31 -0
endoreg_db/models/label/video_segmentation_labelset.py +27 -0
endoreg_db/models/media/__init__.py +16 -0
endoreg_db/models/media/frame/__init__.py +3 -0
endoreg_db/models/media/frame/frame.py +111 -0
endoreg_db/models/media/pdf/__init__.py +11 -0
endoreg_db/models/media/pdf/raw_pdf.py +757 -0
endoreg_db/models/media/pdf/report_file.py +162 -0
endoreg_db/models/media/pdf/report_reader/__init__.py +7 -0
endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +19 -19
endoreg_db/models/media/video/__init__.py +8 -0
endoreg_db/models/media/video/create_from_file.py +358 -0
endoreg_db/models/media/video/pipe_1.py +213 -0
endoreg_db/models/media/video/pipe_2.py +105 -0
endoreg_db/models/media/video/refactor_plan.md +0 -0
endoreg_db/models/media/video/video_file.py +825 -0
endoreg_db/models/media/video/video_file_ai.py +443 -0
endoreg_db/models/media/video/video_file_anonymize.py +349 -0
endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +141 -0
endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
endoreg_db/models/media/video/video_file_frames.py +0 -0
endoreg_db/models/media/video/video_file_io.py +168 -0
endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
endoreg_db/models/media/video/video_file_segments.py +209 -0
endoreg_db/models/media/video/video_metadata.py +65 -0
endoreg_db/models/media/video/video_processing.py +152 -0
endoreg_db/models/medical/__init__.py +146 -0
endoreg_db/models/medical/contraindication/__init__.py +17 -0
endoreg_db/models/medical/disease.py +156 -0
endoreg_db/models/medical/event.py +137 -0
endoreg_db/models/medical/examination/__init__.py +9 -0
endoreg_db/models/medical/examination/examination.py +148 -0
endoreg_db/models/medical/examination/examination_indication.py +278 -0
endoreg_db/models/medical/examination/examination_time.py +49 -0
endoreg_db/models/medical/examination/examination_time_type.py +41 -0
endoreg_db/models/medical/examination/examination_type.py +48 -0
endoreg_db/models/medical/finding/__init__.py +18 -0
endoreg_db/models/medical/finding/finding.py +96 -0
endoreg_db/models/medical/finding/finding_classification.py +142 -0
endoreg_db/models/medical/finding/finding_intervention.py +52 -0
endoreg_db/models/medical/finding/finding_type.py +35 -0
endoreg_db/models/medical/hardware/__init__.py +8 -0
endoreg_db/models/medical/hardware/endoscope.py +65 -0
endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +182 -143
endoreg_db/models/medical/laboratory/__init__.py +5 -0
endoreg_db/models/medical/laboratory/lab_value.py +419 -0
endoreg_db/models/medical/medication/__init__.py +19 -0
endoreg_db/models/medical/medication/medication.py +31 -0
endoreg_db/models/medical/medication/medication_indication.py +50 -0
endoreg_db/models/medical/medication/medication_indication_type.py +39 -0
endoreg_db/models/medical/medication/medication_intake_time.py +44 -0
endoreg_db/models/medical/medication/medication_schedule.py +45 -0
endoreg_db/models/medical/organ/__init__.py +35 -0
endoreg_db/models/medical/patient/__init__.py +56 -0
endoreg_db/models/medical/patient/medication_examples.py +38 -0
endoreg_db/models/medical/patient/patient_disease.py +63 -0
endoreg_db/models/medical/patient/patient_event.py +75 -0
endoreg_db/models/medical/patient/patient_examination.py +249 -0
endoreg_db/models/medical/patient/patient_examination_indication.py +44 -0
endoreg_db/models/medical/patient/patient_finding.py +357 -0
endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
endoreg_db/models/medical/patient/patient_finding_intervention.py +40 -0
endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +222 -176
endoreg_db/models/medical/patient/patient_medication.py +104 -0
endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
endoreg_db/models/medical/risk/__init__.py +7 -0
endoreg_db/models/medical/risk/risk.py +72 -0
endoreg_db/models/medical/risk/risk_type.py +51 -0
endoreg_db/models/metadata/__init__.py +19 -0
endoreg_db/models/metadata/frame_ocr_result.py +0 -0
endoreg_db/models/metadata/model_meta.py +206 -0
endoreg_db/models/metadata/model_meta_logic.py +343 -0
endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +89 -70
endoreg_db/models/metadata/sensitive_meta.py +288 -0
endoreg_db/models/metadata/sensitive_meta_logic.py +1048 -0
endoreg_db/models/metadata/video_meta.py +332 -0
endoreg_db/models/metadata/video_prediction_logic.py +190 -0
endoreg_db/models/metadata/video_prediction_meta.py +270 -0
endoreg_db/models/other/__init__.py +40 -5
endoreg_db/models/other/distribution/__init__.py +44 -0
endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
endoreg_db/models/other/distribution/date_value_distribution.py +89 -0
endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
endoreg_db/models/other/distribution/numeric_value_distribution.py +125 -0
endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
endoreg_db/models/other/emission/__init__.py +5 -0
endoreg_db/models/other/emission/emission_factor.py +94 -0
endoreg_db/models/{persons → other}/gender.py +27 -22
endoreg_db/models/other/information_source.py +159 -0
endoreg_db/models/other/material.py +28 -16
endoreg_db/models/other/resource.py +21 -17
endoreg_db/models/other/tag.py +27 -0
endoreg_db/models/other/transport_route.py +33 -21
endoreg_db/models/{unit.py → other/unit.py} +32 -22
endoreg_db/models/other/waste.py +27 -20
endoreg_db/models/requirement/__init__.py +11 -0
endoreg_db/models/requirement/requirement.py +767 -0
endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +95 -0
endoreg_db/models/requirement/requirement_operator.py +176 -0
endoreg_db/models/requirement/requirement_set.py +287 -0
endoreg_db/models/rule/__init__.py +13 -0
endoreg_db/models/{rules → rule}/rule.py +27 -24
endoreg_db/models/{rules → rule}/rule_applicator.py +224 -224
endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +16 -18
endoreg_db/models/{rules → rule}/rule_type.py +19 -21
endoreg_db/models/{rules → rule}/ruleset.py +17 -19
endoreg_db/models/state/__init__.py +12 -0
endoreg_db/models/state/abstract.py +11 -0
endoreg_db/models/state/audit_ledger.py +150 -0
endoreg_db/models/state/label_video_segment.py +22 -0
endoreg_db/models/state/raw_pdf.py +187 -0
endoreg_db/models/state/sensitive_meta.py +46 -0
endoreg_db/models/state/video.py +232 -0
endoreg_db/models/upload_job.py +99 -0
endoreg_db/models/utils.py +135 -0
endoreg_db/queries/__init__.py +4 -4
endoreg_db/queries/annotations/__init__.py +2 -2
endoreg_db/queries/annotations/legacy.py +158 -159
endoreg_db/renames.yml +8 -0
endoreg_db/root_urls.py +9 -0
endoreg_db/schemas/__init__.py +0 -0
endoreg_db/schemas/examination_evaluation.py +27 -0
endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
endoreg_db/serializers/__init__.py +118 -10
endoreg_db/serializers/_old/raw_pdf_meta_validation.py +223 -0
endoreg_db/serializers/_old/raw_video_meta_validation.py +179 -0
endoreg_db/serializers/_old/video.py +71 -0
endoreg_db/serializers/administration/__init__.py +14 -0
endoreg_db/serializers/administration/ai/__init__.py +10 -0
endoreg_db/serializers/administration/ai/active_model.py +10 -0
endoreg_db/serializers/administration/ai/ai_model.py +18 -0
endoreg_db/serializers/administration/ai/model_type.py +10 -0
endoreg_db/serializers/administration/center.py +9 -0
endoreg_db/serializers/administration/gender.py +9 -0
endoreg_db/serializers/anonymization.py +69 -0
endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
endoreg_db/serializers/examination/__init__.py +10 -0
endoreg_db/serializers/examination/base.py +46 -0
endoreg_db/serializers/examination/dropdown.py +21 -0
endoreg_db/serializers/examination_serializer.py +12 -0
endoreg_db/serializers/finding/__init__.py +5 -0
endoreg_db/serializers/finding/finding.py +54 -0
endoreg_db/serializers/finding_classification/__init__.py +7 -0
endoreg_db/serializers/finding_classification/choice.py +19 -0
endoreg_db/serializers/finding_classification/classification.py +13 -0
endoreg_db/serializers/label/__init__.py +7 -0
endoreg_db/serializers/label/image_classification_annotation.py +62 -0
endoreg_db/serializers/label/label.py +15 -0
endoreg_db/serializers/label_video_segment/__init__.py +7 -0
endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
endoreg_db/serializers/meta/__init__.py +19 -0
endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
endoreg_db/serializers/meta/report_meta.py +53 -0
endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
endoreg_db/serializers/meta/video_meta.py +39 -0
endoreg_db/serializers/misc/__init__.py +14 -0
endoreg_db/serializers/misc/file_overview.py +182 -0
endoreg_db/serializers/misc/sensitive_patient_data.py +120 -0
endoreg_db/serializers/misc/stats.py +33 -0
endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
endoreg_db/serializers/misc/upload_job.py +71 -0
endoreg_db/serializers/patient/__init__.py +11 -0
endoreg_db/serializers/patient/patient.py +86 -0
endoreg_db/serializers/patient/patient_dropdown.py +27 -0
endoreg_db/serializers/patient_examination/__init__.py +7 -0
endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
endoreg_db/serializers/patient_finding/__init__.py +15 -0
endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
endoreg_db/serializers/pdf/__init__.py +5 -0
endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
endoreg_db/serializers/report/__init__.py +9 -0
endoreg_db/serializers/report/mixins.py +45 -0
endoreg_db/serializers/report/report.py +105 -0
endoreg_db/serializers/report/report_list.py +22 -0
endoreg_db/serializers/report/secure_file_url.py +26 -0
endoreg_db/serializers/requirements/requirement_schema.py +25 -0
endoreg_db/serializers/requirements/requirement_sets.py +29 -0
endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
endoreg_db/serializers/video/__init__.py +7 -0
endoreg_db/serializers/video/segmentation.py +263 -0
endoreg_db/serializers/video/video_file_brief.py +10 -0
endoreg_db/serializers/video/video_file_detail.py +83 -0
endoreg_db/serializers/video/video_file_list.py +67 -0
endoreg_db/serializers/video/video_metadata.py +105 -0
endoreg_db/serializers/video/video_processing_history.py +153 -0
endoreg_db/serializers/video_examination.py +198 -0
endoreg_db/services/__init__.py +5 -0
endoreg_db/services/anonymization.py +223 -0
endoreg_db/services/examination_evaluation.py +149 -0
endoreg_db/services/finding_description_service.py +0 -0
endoreg_db/services/lookup_service.py +411 -0
endoreg_db/services/lookup_store.py +266 -0
endoreg_db/services/pdf_import.py +1382 -0
endoreg_db/services/polling_coordinator.py +288 -0
endoreg_db/services/pseudonym_service.py +89 -0
endoreg_db/services/requirements_object.py +147 -0
endoreg_db/services/segment_sync.py +155 -0
endoreg_db/services/storage_aware_video_processor.py +344 -0
endoreg_db/services/video_import.py +1259 -0
endoreg_db/tasks/upload_tasks.py +207 -0
endoreg_db/tasks/video_ingest.py +157 -0
endoreg_db/tasks/video_processing_tasks.py +327 -0
endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
endoreg_db/templates/admin/start_examination.html +12 -0
endoreg_db/templates/timeline.html +176 -0
endoreg_db/urls/__init__.py +83 -0
endoreg_db/urls/anonymization.py +32 -0
endoreg_db/urls/auth.py +16 -0
endoreg_db/urls/classification.py +39 -0
endoreg_db/urls/examination.py +54 -0
endoreg_db/urls/files.py +6 -0
endoreg_db/urls/label_video_segment_validate.py +33 -0
endoreg_db/urls/label_video_segments.py +46 -0
endoreg_db/urls/media.py +227 -0
endoreg_db/urls/patient.py +19 -0
endoreg_db/urls/report.py +48 -0
endoreg_db/urls/requirements.py +13 -0
endoreg_db/urls/sensitive_meta.py +0 -0
endoreg_db/urls/stats.py +46 -0
endoreg_db/urls/upload.py +20 -0
endoreg_db/urls/video.py +61 -0
endoreg_db/urls.py +9 -0
endoreg_db/utils/__init__.py +88 -1
endoreg_db/utils/ai/__init__.py +9 -0
endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +5 -8
endoreg_db/utils/ai/inference_dataset.py +52 -0
endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
endoreg_db/utils/ai/postprocess.py +63 -0
endoreg_db/utils/ai/predict.py +291 -0
endoreg_db/utils/ai/preprocess.py +68 -0
endoreg_db/utils/calc_duration_seconds.py +24 -0
endoreg_db/utils/case_generator/__init__.py +0 -0
endoreg_db/utils/case_generator/case_generator.py +159 -0
endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
endoreg_db/utils/case_generator/utils.py +30 -0
endoreg_db/utils/check_video_files.py +148 -0
endoreg_db/utils/cropping.py +28 -28
endoreg_db/utils/dataloader.py +175 -92
endoreg_db/utils/dates.py +60 -0
endoreg_db/utils/env.py +33 -0
endoreg_db/utils/extract_specific_frames.py +72 -0
endoreg_db/utils/file_operations.py +58 -30
endoreg_db/utils/fix_video_path_direct.py +141 -0
endoreg_db/utils/frame_anonymization_utils.py +463 -0
endoreg_db/utils/hashs.py +153 -34
endoreg_db/utils/links/__init__.py +0 -0
endoreg_db/utils/links/requirement_link.py +193 -0
endoreg_db/utils/mime_types.py +0 -0
endoreg_db/utils/names.py +76 -0
endoreg_db/utils/ocr.py +190 -197
endoreg_db/utils/parse_and_generate_yaml.py +46 -0
endoreg_db/utils/paths.py +95 -0
endoreg_db/utils/permissions.py +143 -0
endoreg_db/utils/pipelines/Readme.md +235 -0
endoreg_db/utils/pipelines/__init__.py +0 -0
endoreg_db/utils/pipelines/process_video_dir.py +120 -0
endoreg_db/utils/product/__init__.py +0 -0
endoreg_db/utils/product/sum_emissions.py +20 -0
endoreg_db/utils/product/sum_weights.py +18 -0
endoreg_db/utils/pydantic_models/__init__.py +6 -0
endoreg_db/utils/pydantic_models/db_config.py +57 -0
endoreg_db/utils/requirement_helpers.py +0 -0
endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
endoreg_db/utils/setup_config.py +177 -0
endoreg_db/utils/translation.py +27 -0
endoreg_db/utils/uuid.py +4 -4
endoreg_db/utils/validate_endo_roi.py +19 -0
endoreg_db/utils/validate_subcategory_dict.py +91 -0
endoreg_db/utils/validate_video_detailed.py +357 -0
endoreg_db/utils/video/__init__.py +26 -0
endoreg_db/utils/video/extract_frames.py +88 -0
endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
endoreg_db/utils/video/names.py +42 -0
endoreg_db/utils/video/streaming_processor.py +312 -0
endoreg_db/utils/video/video_splitter.py +94 -0
endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
endoreg_db/views/__init__.py +275 -0
endoreg_db/views/anonymization/__init__.py +27 -0
endoreg_db/views/anonymization/media_management.py +454 -0
endoreg_db/views/anonymization/overview.py +216 -0
endoreg_db/views/anonymization/validate.py +107 -0
endoreg_db/views/auth/__init__.py +13 -0
endoreg_db/views/auth/keycloak.py +113 -0
endoreg_db/views/examination/__init__.py +33 -0
endoreg_db/views/examination/examination.py +37 -0
endoreg_db/views/examination/examination_manifest_cache.py +26 -0
endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
endoreg_db/views/examination/get_finding_classifications.py +36 -0
endoreg_db/views/examination/get_findings.py +41 -0
endoreg_db/views/examination/get_instruments.py +18 -0
endoreg_db/views/examination/get_interventions.py +14 -0
endoreg_db/views/finding/__init__.py +9 -0
endoreg_db/views/finding/finding.py +112 -0
endoreg_db/views/finding/get_classifications.py +14 -0
endoreg_db/views/finding/get_interventions.py +17 -0
endoreg_db/views/finding_classification/__init__.py +13 -0
endoreg_db/views/finding_classification/base.py +0 -0
endoreg_db/views/finding_classification/finding_classification.py +42 -0
endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
endoreg_db/views/label/__init__.py +5 -0
endoreg_db/views/label/label.py +15 -0
endoreg_db/views/label_video_segment/__init__.py +16 -0
endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
endoreg_db/views/label_video_segment/validate.py +226 -0
endoreg_db/views/media/__init__.py +45 -0
endoreg_db/views/media/pdf_media.py +388 -0
endoreg_db/views/media/segments.py +71 -0
endoreg_db/views/media/sensitive_metadata.py +314 -0
endoreg_db/views/media/video_media.py +272 -0
endoreg_db/views/media/video_segments.py +524 -0
endoreg_db/views/meta/__init__.py +15 -0
endoreg_db/views/meta/available_files_list.py +146 -0
endoreg_db/views/meta/report_meta.py +53 -0
endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
endoreg_db/views/meta/sensitive_meta_list.py +104 -0
endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
endoreg_db/views/misc/__init__.py +63 -0
endoreg_db/views/misc/center.py +13 -0
endoreg_db/views/misc/csrf.py +7 -0
endoreg_db/views/misc/gender.py +14 -0
endoreg_db/views/misc/secure_file_serving_view.py +80 -0
endoreg_db/views/misc/secure_file_url_view.py +84 -0
endoreg_db/views/misc/secure_url_validate.py +79 -0
endoreg_db/views/misc/stats.py +220 -0
endoreg_db/views/misc/translation.py +182 -0
endoreg_db/views/misc/upload_views.py +240 -0
endoreg_db/views/patient/__init__.py +5 -0
endoreg_db/views/patient/patient.py +210 -0
endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
endoreg_db/views/patient_examination/__init__.py +11 -0
endoreg_db/views/patient_examination/patient_examination.py +140 -0
endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
endoreg_db/views/patient_examination/video.py +194 -0
endoreg_db/views/patient_finding/__init__.py +7 -0
endoreg_db/views/patient_finding/base.py +0 -0
endoreg_db/views/patient_finding/patient_finding.py +64 -0
endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
endoreg_db/views/patient_finding_classification/__init__.py +5 -0
endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
endoreg_db/views/patient_finding_location/__init__.py +5 -0
endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
endoreg_db/views/pdf/__init__.py +8 -0
endoreg_db/views/pdf/pdf_stream.py +187 -0
endoreg_db/views/pdf/reimport.py +177 -0
endoreg_db/views/report/__init__.py +9 -0
endoreg_db/views/report/report_list.py +112 -0
endoreg_db/views/report/report_with_secure_url.py +28 -0
endoreg_db/views/report/start_examination.py +7 -0
endoreg_db/views/requirement/__init__.py +10 -0
endoreg_db/views/requirement/evaluate.py +279 -0
endoreg_db/views/requirement/lookup.py +367 -0
endoreg_db/views/requirement/lookup_store.py +252 -0
endoreg_db/views/requirement_lookup/lookup.py +0 -0
endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
endoreg_db/views/stats/__init__.py +13 -0
endoreg_db/views/stats/stats_views.py +229 -0
endoreg_db/views/video/__init__.py +59 -0
endoreg_db/views/video/correction.py +530 -0
endoreg_db/views/video/reimport.py +195 -0
endoreg_db/views/video/segmentation.py +274 -0
endoreg_db/views/video/task_status.py +49 -0
endoreg_db/views/video/timeline.py +46 -0
endoreg_db/views/video/video_analyze.py +52 -0
endoreg_db/views/video/video_apply_mask.py +48 -0
endoreg_db/views/video/video_correction.py +21 -0
endoreg_db/views/video/video_download_processed.py +58 -0
endoreg_db/views/video/video_examination_viewset.py +242 -0
endoreg_db/views/video/video_meta.py +29 -0
endoreg_db/views/video/video_processing_history.py +24 -0
endoreg_db/views/video/video_remove_frames.py +48 -0
endoreg_db/views/video/video_stream.py +306 -0
endoreg_db/views.py +0 -3
endoreg_db-0.8.6.1.dist-info/METADATA +383 -0
endoreg_db-0.8.6.1.dist-info/RECORD +793 -0
{endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info}/WHEEL +1 -1
{endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info/licenses}/LICENSE +674 -674
endoreg_db/data/active_model/data.yaml +0 -3
endoreg_db/data/label/label-set/data.yaml +0 -18
endoreg_db/management/commands/_load_model_template.py +0 -41
endoreg_db/management/commands/delete_all.py +0 -18
endoreg_db/management/commands/delete_legacy_images.py +0 -19
endoreg_db/management/commands/delete_legacy_videos.py +0 -17
endoreg_db/management/commands/extract_legacy_video_frames.py +0 -18
endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
endoreg_db/management/commands/fix_auth_permission.py +0 -20
endoreg_db/management/commands/import_legacy_images.py +0 -94
endoreg_db/management/commands/import_legacy_videos.py +0 -76
endoreg_db/management/commands/load_active_model_data.py +0 -45
endoreg_db/management/commands/load_endoscopy_processor_data.py +0 -45
endoreg_db/management/commands/load_g_play_data.py +0 -113
endoreg_db/management/commands/load_label_data.py +0 -67
endoreg_db/management/commands/load_medication_indication_data.py +0 -63
endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
endoreg_db/migrations/0002_rawvideofile.py +0 -26
endoreg_db/migrations/0003_rawvideofile_frames_required.py +0 -18
endoreg_db/migrations/0004_rename_hash_rawvideofile_video_hash.py +0 -18
endoreg_db/migrations/0005_ffmpegmeta_remove_videoimportmeta_center_and_more.py +0 -56
endoreg_db/migrations/0006_rawvideofile_center_alter_videometa_processor.py +0 -25
endoreg_db/migrations/0007_rawvideofile_processor.py +0 -19
endoreg_db/migrations/0008_rename_frames_required_rawvideofile_state_frames_required.py +0 -18
endoreg_db/migrations/0009_sensitivemeta_rawvideofile_sensitive_meta.py +0 -31
endoreg_db/migrations/0010_rename_endoscope_serial_number_sensitivemeta_endoscope_sn.py +0 -18
endoreg_db/migrations/0011_rawvideofile_state_sensitive_data_retrieved.py +0 -18
endoreg_db/migrations/0012_rawvideofile_prediction_dir_and_more.py +0 -109
endoreg_db/migrations/0013_rawpdffile.py +0 -31
endoreg_db/migrations/0014_pdftype_alter_rawpdffile_file_pdfmeta.py +0 -38
endoreg_db/migrations/0015_rename_report_processed_rawpdffile_state_report_processed_and_more.py +0 -31
endoreg_db/migrations/0016_rawpdffile_state_report_processing_required.py +0 -18
endoreg_db/migrations/0017_firstname_lastname_center_first_names_and_more.py +0 -37
endoreg_db/migrations/0018_reportreaderflag_reportreaderconfig.py +0 -37
endoreg_db/migrations/0019_pdftype_cut_off_above_lines_and_more.py +0 -42
endoreg_db/migrations/0020_rename_endoscopy_info_line_pdftype_endoscope_info_line.py +0 -18
endoreg_db/migrations/0021_alter_pdftype_endoscope_info_line.py +0 -19
endoreg_db/migrations/0022_alter_pdftype_endoscope_info_line.py +0 -19
endoreg_db/migrations/0023_ttoquestionnaire_alter_pdftype_endoscope_info_line.py +0 -59
endoreg_db/migrations/0024_remove_ttoquestionnaire_infections_and_more.py +0 -27
endoreg_db/migrations/0025_event_alter_rawpdffile_file_patientevent.py +0 -42
endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py +0 -166
endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py +0 -38
endoreg_db/migrations/0028_alter_unit_abbreviation.py +0 -18
endoreg_db/migrations/0029_medicationintaketime_and_more.py +0 -75
endoreg_db/migrations/0030_medicationindicationtype_and_more.py +0 -101
endoreg_db/migrations/0031_rename_adapt_to_liver_function_medication_adapt_to_age_and_more.py +0 -38
endoreg_db/migrations/0032_alter_medicationschedule_therapy_duration_d.py +0 -18
endoreg_db/migrations/0033_medicationindication_sources.py +0 -18
endoreg_db/migrations/0034_alter_rawpdffile_file.py +0 -20
endoreg_db/migrations/0035_alter_medicationindication_sources.py +0 -18
endoreg_db/migrations/0036_alter_rawpdffile_file.py +0 -20
endoreg_db/migrations/0037_alter_medicationindication_sources.py +0 -18
endoreg_db/migrations/0038_emissionfactor_material_product_productgroup_and_more.py +0 -164
endoreg_db/migrations/0039_referenceproduct_name.py +0 -19
endoreg_db/migrations/0040_quizanswertype_quizquestiontype_quizquestion_and_more.py +0 -50
endoreg_db/migrations/0041_gender_patientmedication_medication_indication_and_more.py +0 -40
endoreg_db/migrations/0042_casetemplateruletype_casetemplaterulevalue_and_more.py +0 -74
endoreg_db/migrations/0043_casetemplatetype_name_de_casetemplatetype_name_en.py +0 -23
endoreg_db/migrations/0044_casetemplateruletype_name_de_and_more.py +0 -23
endoreg_db/migrations/0045_casetemplaterulevalue_value_type.py +0 -19
endoreg_db/migrations/0046_casetemplaterulevalue_target_field.py +0 -18
endoreg_db/migrations/0047_casetemplaterule_target_model.py +0 -18
endoreg_db/migrations/0048_remove_casetemplaterule_chained_rules_and_more.py +0 -22
endoreg_db/migrations/0049_remove_casetemplaterule_rule_values.py +0 -17
endoreg_db/migrations/0050_casetemplaterule_rule_values.py +0 -18
endoreg_db/migrations/0051_remove_casetemplaterule_calling_rules_and_more.py +0 -27
endoreg_db/migrations/0052_rename_case_template_type_casetemplate_template_type.py +0 -18
endoreg_db/migrations/0053_patientlabsampletype_patientlabsample_and_more.py +0 -38
endoreg_db/migrations/0054_multiplecategoricalvaluedistribution_and_more.py +0 -69
endoreg_db/migrations/0055_remove_casetemplaterule_rule_values_and_more.py +0 -59
endoreg_db/migrations/0056_datevaluedistribution_and_more.py +0 -32
endoreg_db/migrations/0057_remove_datevaluedistribution_max_date_and_more.py +0 -72
endoreg_db/migrations/0058_datevaluedistribution_description_and_more.py +0 -28
endoreg_db/migrations/0059_casetemplaterule_rule_values.py +0 -18
endoreg_db/migrations/0060_labvalue__default_date_value_distribution_and_more.py +0 -44
endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py +0 -24
endoreg_db/migrations/0062_labvalue_numeric_precision.py +0 -18
endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py +0 -18
endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py +0 -23
endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py +0 -58
endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py +0 -29
endoreg_db/migrations/0067_alter_medicationindication_indication_type.py +0 -19
endoreg_db/models/ai_model/__init__.py +0 -3
endoreg_db/models/ai_model/active_model.py +0 -9
endoreg_db/models/ai_model/model_meta.py +0 -24
endoreg_db/models/annotation/__init__.py +0 -2
endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -80
endoreg_db/models/annotation/image_classification.py +0 -27
endoreg_db/models/center/center.py +0 -25
endoreg_db/models/center/center_product.py +0 -34
endoreg_db/models/center/center_resource.py +0 -19
endoreg_db/models/center/center_waste.py +0 -11
endoreg_db/models/data_file/__init__.py +0 -6
endoreg_db/models/data_file/base_classes/__init__.py +0 -2
endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -51
endoreg_db/models/data_file/base_classes/abstract_video.py +0 -201
endoreg_db/models/data_file/frame.py +0 -45
endoreg_db/models/data_file/import_classes/__init__.py +0 -32
endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -188
endoreg_db/models/data_file/import_classes/raw_video.py +0 -343
endoreg_db/models/data_file/metadata/__init__.py +0 -3
endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -31
endoreg_db/models/data_file/metadata/video_meta.py +0 -133
endoreg_db/models/data_file/report_file.py +0 -89
endoreg_db/models/data_file/video/__init__.py +0 -7
endoreg_db/models/data_file/video/import_meta.py +0 -25
endoreg_db/models/data_file/video/video.py +0 -25
endoreg_db/models/data_file/video_segment.py +0 -107
endoreg_db/models/disease.py +0 -56
endoreg_db/models/emission/__init__.py +0 -1
endoreg_db/models/emission/emission_factor.py +0 -20
endoreg_db/models/event.py +0 -22
endoreg_db/models/examination/__init__.py +0 -4
endoreg_db/models/examination/examination.py +0 -26
endoreg_db/models/examination/examination_time.py +0 -27
endoreg_db/models/examination/examination_time_type.py +0 -24
endoreg_db/models/examination/examination_type.py +0 -18
endoreg_db/models/hardware/__init__.py +0 -2
endoreg_db/models/hardware/endoscope.py +0 -44
endoreg_db/models/information_source.py +0 -29
endoreg_db/models/laboratory/__init__.py +0 -1
endoreg_db/models/laboratory/lab_value.py +0 -102
endoreg_db/models/legacy_data/__init__.py +0 -3
endoreg_db/models/legacy_data/image.py +0 -34
endoreg_db/models/medication/__init__.py +0 -1
endoreg_db/models/medication/medication.py +0 -148
endoreg_db/models/other/distribution.py +0 -215
endoreg_db/models/patient_examination/__init__.py +0 -35
endoreg_db/models/permissions/__init__.py +0 -44
endoreg_db/models/persons/__init__.py +0 -7
endoreg_db/models/persons/examiner/__init__.py +0 -2
endoreg_db/models/persons/examiner/examiner.py +0 -16
endoreg_db/models/persons/examiner/examiner_type.py +0 -2
endoreg_db/models/persons/patient/__init__.py +0 -8
endoreg_db/models/persons/patient/case/case.py +0 -30
endoreg_db/models/persons/patient/patient.py +0 -216
endoreg_db/models/persons/patient/patient_disease.py +0 -16
endoreg_db/models/persons/patient/patient_event.py +0 -22
endoreg_db/models/persons/patient/patient_lab_sample.py +0 -106
endoreg_db/models/persons/patient/patient_medication.py +0 -44
endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -28
endoreg_db/models/persons/portal_user_information.py +0 -27
endoreg_db/models/prediction/__init__.py +0 -2
endoreg_db/models/prediction/image_classification.py +0 -37
endoreg_db/models/prediction/video_prediction_meta.py +0 -244
endoreg_db/models/product/__init__.py +0 -5
endoreg_db/models/product/product.py +0 -97
endoreg_db/models/product/product_group.py +0 -19
endoreg_db/models/product/product_material.py +0 -24
endoreg_db/models/questionnaires/__init__.py +0 -114
endoreg_db/models/quiz/__init__.py +0 -2
endoreg_db/models/quiz/quiz_answer.py +0 -41
endoreg_db/models/quiz/quiz_question.py +0 -54
endoreg_db/models/report_reader/__init__.py +0 -2
endoreg_db/models/report_reader/report_reader_config.py +0 -53
endoreg_db/models/rules/__init__.py +0 -5
endoreg_db/queries/get/__init__.py +0 -6
endoreg_db/queries/get/center.py +0 -42
endoreg_db/queries/get/model.py +0 -13
endoreg_db/queries/get/patient.py +0 -14
endoreg_db/queries/get/patient_examination.py +0 -20
endoreg_db/queries/get/report_file.py +0 -33
endoreg_db/queries/get/video.py +0 -31
endoreg_db/serializers/ai_model.py +0 -19
endoreg_db/serializers/annotation.py +0 -17
endoreg_db/serializers/center.py +0 -11
endoreg_db/serializers/examination.py +0 -33
endoreg_db/serializers/frame.py +0 -13
endoreg_db/serializers/hardware.py +0 -21
endoreg_db/serializers/label.py +0 -22
endoreg_db/serializers/patient.py +0 -10
endoreg_db/serializers/prediction.py +0 -15
endoreg_db/serializers/report_file.py +0 -7
endoreg_db/serializers/video.py +0 -27
endoreg_db/tests.py +0 -3
endoreg_db/utils/legacy_ocr.py +0 -201
endoreg_db/utils/video_metadata.py +0 -87
endoreg_db-0.3.6.dist-info/METADATA +0 -33
endoreg_db-0.3.6.dist-info/RECORD +0 -357
/endoreg_db/{models/persons/patient/case/__init__.py → api/serializers/finding_descriptions.py} +0 -0
/endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
/endoreg_db/{queries/get/prediction.py → config/__init__.py} +0 -0
/endoreg_db/{queries/get/video_import_meta.py → data/case_template/rule_value/.init} +0 -0
/endoreg_db/{queries/get/video_prediction_meta.py → data/distribution/multiple_categorical/.init} +0 -0

endoreg_db/data/requirement/event_requirements.yaml ADDED Viewed

@@ -0,0 +1,145 @@
+# /home/admin/dev/endo-ai/endoreg-db/endoreg_db/data/requirement/event_requirements.yaml
+- model: endoreg_db.requirement
+  fields:
+    name: "event_coro_des_implantation_exists"
+    name_de: "Ereignis Koronarstent-Implantation (DES) vorhanden"
+    name_en: "Event Coronary Stent Implantation (DES) exists"
+    description: "Checks if a 'coro_des_implantation' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "coro_des_implantation"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_coro_bms_implantation_exists"
+    name_de: "Ereignis Koronarstent-Implantation (BMS) vorhanden"
+    name_en: "Event Coronary Stent Implantation (BMS) exists"
+    description: "Checks if a 'coro_bms_implantation' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "coro_bms_implantation"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_pulmonary_embolism_exists"
+    name_de: "Ereignis Lungenembolie vorhanden"
+    name_en: "Event Pulmonary Embolism exists"
+    description: "Checks if a 'pulmonary_embolism' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "pulmonary_embolism"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_deep_vein_thrombosis_exists"
+    name_de: "Ereignis Tiefe Beinvenenthrombose vorhanden"
+    name_en: "Event Deep Vein Thrombosis exists"
+    description: "Checks if a 'deep_vein_thrombosis' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "deep_vein_thrombosis"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_stroke_exists"
+    name_de: "Ereignis Schlaganfall vorhanden"
+    name_en: "Event Stroke exists"
+    description: "Checks if a 'stroke' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "stroke"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_transient_ischemic_attack_exists"
+    name_de: "Ereignis Transitorische ischämische Attacke vorhanden"
+    name_en: "Event Transient Ischemic Attack exists"
+    description: "Checks if a 'transient_ischemic_attack' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "transient_ischemic_attack"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_hip_replacement_surgery_exists"
+    name_de: "Ereignis Hüft-TEP Operation vorhanden"
+    name_en: "Event Hip replacement surgery exists"
+    description: "Checks if a 'hip_replacement_surgery' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "hip_replacement_surgery"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_knee_replacement_surgery_exists"
+    name_de: "Ereignis Knie-TEP Operation vorhanden"
+    name_en: "Event Knee replacement surgery exists"
+    description: "Checks if a 'knee_replacement_surgery' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "knee_replacement_surgery"
+- model: endoreg_db.requirement
+  fields:
+    name: "event_recurrent_thrombembolism_exists"
+    name_de: "Ereignis Rezidivierende Thrombembolien vorhanden"
+    name_en: "Event Recurrent Thrombembolism exists"
+    description: "Checks if a 'recurrent_thrombembolism' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "recurrent_thrombembolism"
+# Example for models_match_any_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "event_stroke_in_last_30_days"
+    name_de: "Ereignis Schlaganfall in den letzten 30 Tagen"
+    name_en: "Event Stroke in the last 30 days"
+    description: "Checks if a 'stroke' event occurred for the patient in the last 30 days."
+    requirement_types: # Defines which input models are expected by Requirement.evaluate()
+      - "patient"
+      - "patient_event" # This tells the system to look for PatientEvent models in the input
+    operators:
+      - models_match_any_in_timeframe
+    events: # This links the Requirement to specific Event models (e.g. "stroke")
+      - "stroke"
+    # Timeframe definition for the operator:
+    numeric_value_min: -30 # Start of timeframe (days ago)
+    numeric_value_max: 0   # End of timeframe (days ago, i.e., today)
+    unit: "days"           # Unit for the timeframe

endoreg_db/data/requirement/finding_colon_polyp.yaml ADDED Viewed

@@ -0,0 +1,50 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "colon_austria_screening_polyp_size"
+    requirement_types:
+      - "patient_examination"
+      - "patient_finding"
+    operators:
+      - "models_match_any"
+    finding_classifications:
+      - "colon_lesion_size_mm"
+      - "colon_lesion_size_austria_categorical"
+- model: endoreg_db.requirement
+  fields:
+    name: "colonoscopy_austria_screening_polyp_location"
+    requirement_types:
+      - "patient_examination"
+      - "patient_finding"
+    operators:
+      - "models_match_any"
+    finding_classifications:
+      - "colonoscopy_austria_screening_location"
+      - "colonoscopy_location_default"
+- model: endoreg_db.requirement
+  fields:
+    name: "colonoscopy_austria_screening_polyp_morphology"
+    operators:
+      - "models_match_any"
+    requirement_types:
+      - "patient_examination"
+      - "patient_finding"
+    finding_classifications:
+      - "colon_lesion_paris"
+      - "colon_lesion_lst"
+      - "colon_lesion_planarity_default"
+- model: endoreg_db.requirement
+  fields:
+    name: "colonoscopy_austria_screening_polyp_histology"
+    requirement_types:
+      - "patient_finding"
+      - "patient_examination"
+    operators:
+      - "models_match_all"
+    finding_classifications:
+      - "colonoscopy_polyp_histology"
+      - "colonoscopy_polyp_histology_dysplasia"
+      - "colonoscopy_histology_dignity"

endoreg_db/data/requirement/gender.yaml ADDED Viewed

@@ -0,0 +1,25 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_gender_is_male"
+    name_de: "Patient ist männlich"
+    name_en: "Patient is male"
+    description: "Checks if the patient is male."
+    requirement_types:
+      - "patient"
+    operators:
+      - models_match_all
+    genders:
+      - "male"
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_gender_is_female"
+    name_de: "Patient ist weiblich"
+    name_en: "Patient is female"
+    description: "Checks if the patient is female."
+    requirement_types:
+      - "patient"
+    operators:
+      - models_match_all
+    genders:
+      - "female"

endoreg_db/data/requirement/lab_value.yaml ADDED Viewed

@@ -0,0 +1,441 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_creatinine_above_normal"
+    name_de: "Laborwert über Normalwert"
+    name_en: "Lab value above normal"
+    description: "Lab value above normal"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_increased
+    lab_values:
+      - "creatinine"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_hb_below_normal"
+    name_de: "Laborwert Hämoglobin unter Normalwert"
+    name_en: "Lab value hemoglobin below normal"
+    description: "Lab value hemoglobin below normal"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_decreased
+    lab_values:
+      - "hemoglobin"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_hb_below_8"
+    name_de: "Laborwert Hämoglobin unter 8"
+    name_en: "Lab value hemoglobin below 8"
+    description: "Lab value hemoglobin below 8"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_lower_than_value
+    lab_values:
+      - "hemoglobin"
+    numeric_value: 8
+    unit: "gram per deciliter"
+# acute kidney injury
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_creatinine_above_1_5"
+    name_de: "Laborwert Kreatinin über 1,5"
+    name_en: "Lab value creatinine above 1.5"
+    description: "Lab value creatinine above 1.5"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_greater_than_value
+    lab_values:
+      - "creatinine"
+    numeric_value: 1.5
+    unit: "miligram per deciliter"
+- model: endoreg_db.requirement
+  fields: # increase by factor 1.5 in 3 days
+    name: "lab_value_latest_creatinine_increased_factor_1_5_in_3_days"
+    name_de: "Laborwert Kreatinin um Faktor 1,5 erhöht innerhalb 3 Tage"
+    name_en: "Lab value creatinine increased by factor 1.5 within 3 days"
+    description: "Lab value creatinine increased by factor 1.5 within 3 days"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_increased_factor_in_timeframe # Corrected operator name
+    lab_values:
+      - "creatinine"
+    numeric_value: 1.5
+    numeric_value_min: -3
+    numeric_value_max: 0
+    unit: "days"
+# Coagulation
+## Prothrombin time above normal
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_prothrombin_time_above_normal"
+    name_de: "Laborwert Prothrombinzeit über Normalwert"
+    name_en: "Lab value prothrombin time above normal"
+    description: "Lab value prothrombin time above normal"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_increased
+    lab_values:
+      - "prothrombin_time"
+## Activated partial thromboplastin time (aPTT) above normal
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_activated_partial_thromboplastin_time_above_normal"
+    name_de: "Laborwert aktivierte partielle Thromboplastinzeit über Normalwert"
+    name_en: "Lab value activated partial thromboplastin time above normal"
+    description: "Lab value activated partial thromboplastin time above normal"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_increased
+    lab_values:
+      - "activated_partial_thromboplastin_time"
+## Fibrinogen below normal
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_alkaline_phosphatase_below_normal"
+    name_de: "Laborwert Alkalische Phosphatase unter Normalwert"
+    name_en: "Lab value alkaline phosphatase below normal"
+    description: "Lab value alkaline phosphatase below normal"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_decreased
+    lab_values:
+      - "alkaline_phosphatase"
+## INR above normal
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_international_normalized_ratio_above_normal"
+    name_de: "Laborwert International Normalisierte Ratio über Normalwert"
+    name_en: "Lab value international normalized ratio above normal"
+    description: "Lab value international normalized ratio above normal"
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_increased
+    lab_values:
+      - "international_normalized_ratio"
+# New Requirement for lab_latest_numeric_normal
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_leukocytes_normal"
+    name_de: "Laborwert Leukozyten im Normalbereich"
+    name_en: "Lab value leukocytes normal"
+    description: "Checks if the latest leukocyte count is within the normal range."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+      - "patient_examination"
+    operators:
+      - lab_latest_numeric_normal
+    lab_values:
+      - "white_blood_cells" # Changed from leukocyte_count
+# New examples for missing operators
+# lab_latest_numeric_decreased_factor_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_latest_platelets_decreased_factor_2_in_7_days"
+    name_de: "Laborwert Thrombozyten um Faktor 2 verringert innerhalb 7 Tage"
+    name_en: "Lab value platelets decreased by factor 2 within 7 days"
+    description: "Lab value platelets decreased by factor 2 within 7 days. Indicates potential significant drop."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_decreased_factor_in_timeframe
+    lab_values:
+      - "platelets" # Changed from platelet_count
+    numeric_value: 2 # Factor
+    numeric_value_min: -7 # Days ago (start of timeframe)
+    numeric_value_max: 0  # Days ago (end of timeframe, i.e., today)
+    unit: "days" # Unit for timeframe
+# lab_latest_numeric_normal_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_potassium_normal_in_last_24_hours"
+    name_de: "Laborwert Kalium im Normalbereich innerhalb der letzten 24 Stunden"
+    name_en: "Lab value potassium normal within the last 24 hours"
+    description: "Checks if potassium was normal at any point in the last 24 hours."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_normal_in_timeframe
+    lab_values:
+      - "potassium"
+    numeric_value_min: -1 # Days ago (start of timeframe, 24 hours)
+    numeric_value_max: 0  # Days ago (end of timeframe, i.e., today)
+    unit: "days"
+# lab_latest_numeric_lower_than_value_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_glucose_below_70_in_last_3_days"
+    name_de: "Laborwert Glukose unter 70 mg/dL innerhalb der letzten 3 Tage"
+    name_en: "Lab value glucose below 70 mg/dL within the last 3 days"
+    description: "Checks for any hypoglycemic event (glucose < 70) in the last 3 days."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_lower_than_value_in_timeframe
+    lab_values:
+      - "glucose"
+    numeric_value: 70 # Threshold value
+    numeric_value_min: -3 # Days ago
+    numeric_value_max: 0  # Days ago
+    unit: "miligram per deciliter" # Unit of the numeric_value, contextually
+# lab_latest_numeric_greater_than_value_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_crp_above_10_in_last_week"
+    name_de: "Laborwert CRP über 10 mg/L innerhalb der letzten Woche"
+    name_en: "Lab value CRP above 10 mg/L within the last week"
+    description: "Checks for elevated CRP (>10 mg/L) at any point in the last week, indicating inflammation."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_greater_than_value_in_timeframe
+    lab_values:
+      - "c_reactive_protein"
+    numeric_value: 10 # Threshold value
+    numeric_value_min: -7 # Days ago
+    numeric_value_max: 0  # Days ago
+    unit: "miligram per liter" # Unit of the numeric_value, contextually
+# lab_latest_categorical_match
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_blood_group_A"
+    name_de: "Laborwert Blutgruppe A"
+    name_en: "Lab value blood group A"
+    description: "Checks if the latest blood group determination is 'A'."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_categorical_match
+    lab_values:
+      - "blood_group" # Assuming 'blood_group' is a LabValue that stores categorical string
+    string_value: "A"
+# lab_latest_categorical_match_substring
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_urine_bacteria_positive"
+    name_de: "Laborwert Urin Bakterien positiv"
+    name_en: "Lab value urine bacteria positive"
+    description: "Checks if the latest urine bacteria result contains 'positiv'."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_categorical_match_substring
+    lab_values:
+      - "urine_bacteria_culture" # Example LabValue name
+    string_value: "positiv" # Substring to search for
+# lab_latest_categorical_match_regex
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_pathogen_detected_staph_aureus"
+    name_de: "Laborwert Erreger Staphylococcus aureus nachgewiesen"
+    name_en: "Lab value pathogen detected Staphylococcus aureus"
+    description: "Checks if 'Staphylococcus aureus' (case-insensitive) is mentioned in the latest pathogen report."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_categorical_match_regex
+    lab_values:
+      - "microbiology_pathogen_report" # Example LabValue name
+    string_value: "(?i)Staphylococcus\\s+aureus" # Regex for case-insensitive match
+# lab_latest_categorical_match_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_drug_test_positive_in_last_month"
+    name_de: "Laborwert Drogentest positiv im letzten Monat"
+    name_en: "Lab value drug test positive in the last month"
+    description: "Checks if any drug test was 'positiv' in the last 30 days."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_categorical_match_in_timeframe
+    lab_values:
+      - "drug_screening_urine" # Example LabValue name
+    string_value: "positiv"
+    numeric_value_min: -30 # Days ago
+    numeric_value_max: 0   # Days ago
+    unit: "days"
+# lab_latest_categorical_match_substring_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_antibiotic_resistance_gentamicin_in_last_year"
+    name_de: "Laborwert Antibiotikaresistenz Gentamicin im letzten Jahr"
+    name_en: "Lab value antibiotic resistance Gentamicin in the last year"
+    description: "Checks if 'Gentamicin' resistance was mentioned in any report in the last year."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_categorical_match_substring_in_timeframe
+    lab_values:
+      - "antibiotic_resistance_report" # Example LabValue name
+    string_value: "Gentamicin"
+    numeric_value_min: -365 # Days ago
+    numeric_value_max: 0    # Days ago
+    unit: "days"
+# lab_latest_categorical_match_regex_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_abnormal_cells_detected_in_cytology_last_6_months"
+    name_de: "Laborwert atypische Zellen in Zytologie in letzten 6 Monaten nachgewiesen"
+    name_en: "Lab value abnormal cells detected in cytology in last 6 months"
+    description: "Checks for mention of 'atypical' or 'malignant' cells in cytology reports in the last 6 months."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_categorical_match_regex_in_timeframe
+    lab_values:
+      - "cytology_report" # Example LabValue name
+    string_value: "(?i)(atypical|malignant)" # Regex for 'atypical' or 'malignant'
+    numeric_value_min: -180 # Days ago (approx 6 months)
+    numeric_value_max: 0    # Days ago
+    unit: "days"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_hb_normal"
+    name_de: "Hämoglobin im Normalbereich"
+    name_en: "Hemoglobin normal"
+    description: "Checks if the latest hemoglobin is within the normal range."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_normal
+    lab_values:
+      - "hemoglobin"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_leukocytes_normal"
+    name_de: "Leukozyten im Normalbereich"
+    name_en: "Leukocytes normal"
+    description: "Checks if the latest leukocyte count is within the normal range."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_normal
+    lab_values:
+      - "white_blood_cells"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_platelets_normal"
+    name_de: "Thrombozyten im Normalbereich"
+    name_en: "Platelets normal"
+    description: "Checks if the latest platelet count is within the normal range."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_normal
+    lab_values:
+      - "platelets"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_creatinine_normal"
+    name_de: "Kreatinin im Normalbereich"
+    name_en: "Creatinine normal"
+    description: "Checks if the latest creatinine is within the normal range."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_normal
+    lab_values:
+      - "creatinine"
+- model: endoreg_db.requirement
+  fields:
+    name: "lab_value_inr_normal"
+    name_de: "INR im Normalbereich"
+    name_en: "INR normal"
+    description: "Checks if the latest INR is within the normal range."
+    requirement_types:
+      - "patient"
+      - "patient_lab_sample"
+      - "patient_lab_value"
+    operators:
+      - lab_latest_numeric_normal
+    lab_values:
+      - "international_normalized_ratio"

endoreg-db 0.3.6__py3-none-any.whl → 0.8.6.1__py3-none-any.whl

Potentially problematic release.

endoreg-db 0.3.6py3-none-any.whl → 0.8.6.1py3-none-any.whl