endoreg-db 0.8.6.4__py3-none-any.whl

endoreg_db/data/case_template/rule_value_type/base_types.yaml

@@ -0,0 +1,59 @@
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "foreign_key"
+    distribution_type: "single_categorical"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "many_to_many"
+    distribution_type: "multiple_categorical"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "object"
+    distribution_type: "single_categorical"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "date"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "integer"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "string"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "boolean"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "float"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "text"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "integer_range"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type 
+  fields:
+    name: "float_range"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "date_range"
+    distribution_type: "numeric"

endoreg_db/data/case_template/template/base.yaml

@@ -0,0 +1,8 @@
+- model: endoreg_db.case_template
+  fields:
+    name: "pre_default_screening_colonoscopy"
+    rules: [
+      "create-patient-default",
+      "create-patient_medication_schedule-anticoagulation-non_valvular_af",
+    ]
+    template_type: "pre_endoscopy"

endoreg_db/data/case_template/template_type/pre_endoscopy.yaml

@@ -0,0 +1,3 @@
+- model: endoreg_db.case_template_type
+  fields:
+    name: "pre_endoscopy"

endoreg_db/data/case_template/tmp/_rule_value

@@ -0,0 +1,13 @@
+- model: endoreg_db.case_template_rule_value
+  fields:
+    name: "diagnosis_value-non_valvular_atrial-fibrillation"
+    target_field: "disease"
+    value_type: "foreign_key"
+    fk_value: "non_valvular_atrial_fibrillation"
+    
+- model: endoreg_db.case_template_rule_value
+  fields:
+    name: "medication_schedule-apixaban-5mg-twice_daily"
+    target_field: "medication_indication"
+    value_type: "foreign_key"
+    fk_value: "te_prevention-recurrent-te-apixaban"

endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml

@@ -0,0 +1,21 @@
+
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient-add_medication_indication-anticoagulation-non_valvular_af"
+    rule_type: "add_one_value"
+    target_model: "endoreg_db.patient_medication_indication"
+    rule_values: [
+      "medication_schedule-apixaban-5mg-twice_daily"
+    ]
+
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_add_diagnosis_atrial-fibrillation"
+    rule_type: "add_one_value"
+    target_model: "endoreg_db.patient_disease"
+    rule_values: [
+      "diagnosis_value-non_valvular_atrial-fibrillation"
+    ]
+    chained_rules: [
+      "patient-add_medication_indication-anticoagulation-non_valvular_af"
+    ]

endoreg_db/data/case_template/tmp/rule/02_create_object.yaml

@@ -0,0 +1,10 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "create-patient-screening_colo"
+    rule_type: "create_object"
+    target_model: "Patient"
+    rule_value_type: "object"
+    target_field: null
+    chained_rules: [
+      "patient-set-gender-random"
+    ]

endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.case_template_type
+  fields:
+    name: "pre_endo-anticoagulation-af-low_risk"
+    template_type: "pre_endoscopy"
+    rules: [
+      "patient_add_diagnosis_atrial-fibrillation"
+    ]

endoreg_db/data/center/data.yaml

@@ -0,0 +1,91 @@
+# center/data.yaml
+
+- model: endoreg_db.center
+  fields:
+    name: "university_hospital_wuerzburg"
+    # name_de: "Universitätsklinikum Würzburg"
+    # name_en: "University Hospital Würzburg"
+
+    first_names: [
+      "Markus",
+      "Linhel",
+      "Rainer",
+      "Hans",
+      "Anja",
+      "Dorothea",
+      "Doro",
+      "Angelika",
+      "Sven",
+      "Theodor",
+      "Alexander",
+      "Mandy",
+      "Kathrin",
+      "Florian",
+      "Philip",
+      "Laura",
+      "Tanja",
+      "Thomas"
+    ]
+    
+    last_names: [
+      "Kozielski",
+      "Reiter",
+      "Purrer",
+      "Hossner",
+      "Kudlich",
+      "Brand",
+      "Weich",
+      "Lux",
+      "Meining",
+      "Hann",
+      "Retzbach",
+      "Hose",
+      "Henniger",
+      "Weich",
+      "Dela Cruz",
+      "Wiesemann",
+      "Wiese",
+      "Sodmann"
+    ]
+- model: endoreg_db.center
+  fields:
+    name: "rbk_stuttgart"
+    # name_de: "Robert-Bosch-Krankenhaus Stuttgart"
+    # name_en: "Robert Bosch Hospital Stuttgart"
+    first_names: [] # many to many; if foreign key, we would just have a string; strings represent "name" attribute
+    last_names: []
+
+# bbk_regensburg
+- model: endoreg_db.center
+  fields:
+    name: "bbk_regensburg"
+    # name_de: "Barmherzige  Brüder Krankenhaus Regensburg"
+    # name_en: "Barmherzige Brüder Hospital Regensburg"
+    first_names: []
+    last_names: []
+
+# uke_hamburg
+- model: endoreg_db.center
+  fields:
+    name: "uke_hamburg"
+    # name_de: "Universitätsklinikum Hamburg-Eppendorf"
+    # name_en: "University Hospital Hamburg-Eppendorf"
+    first_names: []
+    last_names: []
+
+# rkh_ludwigsburg
+- model: endoreg_db.center
+  fields:
+    name: "rkh_ludwigsburg"
+    # name_de: "RKH Krankenhaus Ludwigsburg"
+    # name_en: "RKH Hospital Ludwigsburg"
+    first_names: []
+    last_names: []
+
+- model: endoreg_db.center
+  fields:
+    name: "endoreg_db_demo"
+    # name_de: "Demo Center"
+    # name_en: "Demo Center"
+    first_names: []
+    last_names: []

endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml

@@ -0,0 +1,144 @@
+- fields:
+    center: university_hospital_wuerzburg
+    name: gas_ukw_2020
+    name_de: Erdgas
+    name_en: Gas
+    quantity: 19000
+    resource: gas
+    transport_emission_factor: transport_resource_emission_ukw_gas
+    unit: liter
+    use_emission_factor: use_resource_emission_ukw_gas
+    year: 2020
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: oil_ukw_2020
+    name_de: "Heizöl"
+    name_en: Oil
+    quantity: 0
+    resource: oil
+    transport_emission_factor: transport_resource_emission_ukw_oil
+    unit: cubic_meter
+    use_emission_factor: use_resource_emission_ukw_oil
+    year: 2020
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: electricity_ukw_extern_2020
+    name_de: Strom (Bezug)
+    name_en: Electricity (extern)
+    quantity: 48000
+    resource: electricity
+    transport_emission_factor: transport_resource_emission_ukw_electricity_extern
+    unit: kilowatt-hours
+    use_emission_factor: use_resource_emission_ukw_electricity_extern
+    year: 2020
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: electricity_ukw_selfmade_2020
+    name_de: Strom (Eigenproduktion)
+    name_en: Electricity (Selfmade)
+    quantity: 22000
+    resource: electricity
+    transport_emission_factor: transport_resource_emission_ukw_electricity_selfmade
+    unit: kilowatt-hours
+    use_emission_factor: use_resource_emission_ukw_electricity_selfmade
+    year: 2020
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: gas_ukw_2021
+    name_de: Erdgas
+    name_en: Gas
+    quantity: 18000
+    resource: gas
+    transport_emission_factor: transport_resource_emission_ukw_gas
+    unit: liter
+    use_emission_factor: use_resource_emission_ukw_gas
+    year: 2021
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: oil_ukw_2021
+    name_de: "Heiz\xF6l"
+    name_en: Oil
+    quantity: 0
+    resource: oil
+    transport_emission_factor: transport_resource_emission_ukw_oil
+    unit: cubic_meter
+    use_emission_factor: use_resource_emission_ukw_oil
+    year: 2021
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: electricity_ukw_extern_2021
+    name_de: Strom (Bezug)
+    name_en: Electricity (extern)
+    quantity: 45000
+    resource: electricity
+    transport_emission_factor: transport_resource_emission_ukw_electricity_extern
+    unit: kilowatt-hours
+    use_emission_factor: use_resource_emission_ukw_electricity_extern
+    year: 2021
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: electricity_ukw_selfmade_2021
+    name_de: Strom (Eigenproduktion)
+    name_en: Electricity (Selfmade)
+    quantity: 22000
+    resource: electricity
+    transport_emission_factor: transport_resource_emission_ukw_electricity_selfmade
+    unit: kilowatt-hours
+    use_emission_factor: use_resource_emission_ukw_electricity_selfmade
+    year: 2021
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: gas_ukw_2022
+    name_de: Erdgas
+    name_en: Gas
+    quantity: 18500
+    resource: gas
+    transport_emission_factor: transport_resource_emission_ukw_gas
+    unit: liter
+    use_emission_factor: use_resource_emission_ukw_gas
+    year: 2022
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: oil_ukw_2022
+    name_de: "Heiz\xF6l"
+    name_en: Oil
+    quantity: 0
+    resource: oil
+    transport_emission_factor: transport_resource_emission_ukw_oil
+    unit: cubic_meter
+    use_emission_factor: use_resource_emission_ukw_oil
+    year: 2022
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: electricity_ukw_extern_2022
+    name_de: Strom (Bezug)
+    name_en: Electricity (extern)
+    quantity: 46000
+    resource: electricity
+    transport_emission_factor: transport_resource_emission_ukw_electricity_extern
+    unit: kilowatt-hours
+    use_emission_factor: use_resource_emission_ukw_electricity_extern
+    year: 2022
+  model: CenterResource
+- fields:
+    center: university_hospital_wuerzburg
+    name: electricity_ukw_selfmade_2022
+    name_de: Strom (Eigenproduktion)
+    name_en: Electricity (Selfmade)
+    quantity: 22000
+    resource: electricity
+    transport_emission_factor: transport_resource_emission_ukw_electricity_selfmade
+    unit: kilowatt-hours
+    use_emission_factor: use_resource_emission_ukw_electricity_selfmade
+    year: 2022
+  model: CenterResource

endoreg_db/data/center_shift/ukw.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.center_shift
+  fields:
+    name: "ukw_endoscopy"
+    name_de: "Endoskopie (Koloskopie Raum)"
+    name_en: "Endoscopy (Colonoscopy Room)"
+    description: "This shift represents the UKW's colonoscopy room."
+    shift: "endoscopy_base"
+    center: "university_hospital_wuerzburg"
+    

endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml

@@ -0,0 +1,48 @@
+- fields:
+    center: university_hospital_wuerzburg
+    emission_factor: waste_emission_general
+    quantity: 10156.3857142857
+    unit: kilogram
+    waste: general_waste
+    year: 2020
+  model: CenterWaste
+- fields:
+    center: university_hospital_wuerzburg
+    emission_factor: waste_emission_medical
+    quantity: 15699.9014285714
+    unit: kilogram
+    waste: medical_waste
+    year: 2020
+  model: CenterWaste
+- fields:
+    center: university_hospital_wuerzburg
+    emission_factor: waste_emission_general
+    quantity: 10156.3857142857
+    unit: kilogram
+    waste: general_waste
+    year: 2021
+  model: CenterWaste
+- fields:
+    center: university_hospital_wuerzburg
+    emission_factor: waste_emission_medical
+    quantity: 15699.9014285714
+    unit: kilogram
+    waste: medical_waste
+    year: 2021
+  model: CenterWaste
+- fields:
+    center: university_hospital_wuerzburg
+    emission_factor: waste_emission_general
+    quantity: 10156.3857142857
+    unit: kilogram
+    waste: general_waste
+    year: 2022
+  model: CenterWaste
+- fields:
+    center: university_hospital_wuerzburg
+    emission_factor: waste_emission_medical
+    quantity: 15699.9014285714
+    unit: kilogram
+    waste: medical_waste
+    year: 2022
+  model: CenterWaste

endoreg_db/data/contraindication/bleeding.yaml

@@ -0,0 +1,11 @@
+- model: endoreg_db.contraindication
+  fields:
+    name: "anticoagulation-therapeutic"
+    description: "Therapeutic anticoagulation"
+
+- model: endoreg_db.contraindication
+  fields:
+    name: "thrombocytopenia-severe"
+    description: "Thrombocyte count < 50.000/µl"
+
+

endoreg_db/data/db_summary.csv

@@ -0,0 +1,58 @@
+Model Name,Total Records
+ModelType,2
+AiModel,1
+Center,6
+FirstName,18
+LastName,17
+NumericValueDistribution,2
+SingleCategoricalValueDistribution,1
+DateValueDistribution,1
+Gender,7
+InformationSource,12
+Unit,38
+Label,27
+LabelSet,3
+LabelType,2
+VideoSegmentationLabel,22
+VideoSegmentationLabelSet,1
+Disease,9
+DiseaseClassification,2
+DiseaseClassificationChoice,9
+Event,10
+Contraindication,2
+Examination,9
+ExaminationType,3
+ExaminationTime,5
+ExaminationTimeType,1
+ExaminationIndication,29
+ExaminationIndicationClassification,13
+ExaminationIndicationClassificationChoice,5
+Finding,8
+FindingType,5
+FindingLocationClassification,2
+FindingLocationClassificationChoice,11
+FindingMorphologyClassificationType,6
+FindingMorphologyClassification,7
+FindingMorphologyClassificationChoice,27
+FindingIntervention,66
+FindingInterventionType,4
+PatientLabSampleType,1
+Risk,7
+RiskType,4
+Medication,10
+MedicationSchedule,10
+MedicationIntakeTime,4
+MedicationIndicationType,9
+MedicationIndication,8
+EndoscopyProcessor,1
+Endoscope,10
+EndoscopeType,2
+LabValue,76
+Organ,5
+PdfType,3
+ReportReaderFlag,12
+RequirementType,23
+Requirement,79
+RequirementOperator,32
+RequirementSetType,3
+RequirementSet,8

endoreg_db/data/disease/cardiovascular.yaml

@@ -0,0 +1,37 @@
+- model: endoreg_db.disease
+  fields:
+    name: "hypertension"
+    name_de: "Arterielle Hypertonie"
+    name_en: "Hypertension"
+
+- model: endoreg_db.disease
+  fields:
+    name: "coronary_artery_disease"
+    name_de: "Koronare Herzkrankheit"
+    name_en: "Coronary Artery Disease"
+
+- model: endoreg_db.disease
+  fields:
+    name: "congestive_heart_failure"
+    name_de: "Chron. Herzinsuffizienz"
+    name_en: "Congestive Heart Failure"
+
+# diabetes mellitus I
+- model: endoreg_db.disease
+  fields:
+    name: "diabetes_mellitus_I"
+    name_de: "Diabetes mellitus Typ I"
+    name_en: "Diabetes Mellitus Type I"
+
+# diabetes mellitus II
+- model: endoreg_db.disease
+  fields:
+    name: "diabetes_mellitus_II"
+    name_de: "Diabetes mellitus Typ II"
+    name_en: "Diabetes Mellitus Type II"
+
+- model: endoreg_db.disease
+  fields:
+    name: "non_valvular_atrial_fibrillation"
+    name_de: "nicht valvuläres Vorhofflimmern"
+    name_en: "non valvular Atrial Fibrillation"

endoreg_db/data/disease/hepatology.yaml

@@ -0,0 +1,5 @@
+- model: endoreg_db.disease
+  fields:
+    name: "liver_cirrhosis"
+    name_de: "Leberzirrhose"
+    name_en: "Liver Cirrhosis"

endoreg_db/data/disease/misc.yaml

@@ -0,0 +1,5 @@
+- model: endoreg_db.disease
+  fields:
+    name: "disease_is_malignoma_unspecified"
+    name_de: "Malignom, nicht näher bezeichnet"
+    name_en: "Malignoma, unspecified"

endoreg_db/data/disease/renal.yaml

@@ -0,0 +1,5 @@
+- model: endoreg_db.disease
+  fields:
+    name: "chronic_kidney_disease"
+    name_de: "Chronische Nierenerkrankung"
+    name_en: "Chronic Kidney Disease"

endoreg_db/data/disease_classification/chronic_kidney_disease.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.disease_classification
+  fields:
+    name: "chronic_kidney_disease_kdigo"
+    name_de: "Chronische Nierenerkrankung (KDIGO)"
+    name_en: "Chronic Kidney Disease (KDIGO)"
+    disease: "chronic_kidney_disease"

endoreg_db/data/disease_classification/coronary_vessel_disease.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.disease_classification
+  fields:
+    name: "coronary_artery_disease_base_classification"
+    name_de: "Koronare Gefäßerkrankung (N-Gefäß-Erkrankung)"
+    name_en: "Coronary Vessel Disease (N-Vessel Disease)"
+    disease: "coronary_artery_disease"

endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml

@@ -0,0 +1,41 @@
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "ckd_kdigo_1"
+    name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 1)"
+    name_en: "Chronic Kidney Disease (KDIGO) (Stage 1)"
+    disease_classification: "chronic_kidney_disease_kdigo"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "ckd_kdigo_2"
+    name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 2)"
+    name_en: "Chronic Kidney Disease (KDIGO) (Stage 2)"
+    disease_classification: "chronic_kidney_disease_kdigo"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "ckd_kdigo_3a"
+    name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 3a)"
+    name_en: "Chronic Kidney Disease (KDIGO) (Stage 3a)"
+    disease_classification: "chronic_kidney_disease_kdigo"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "ckd_kdigo_3b"
+    name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 3b)"
+    name_en: "Chronic Kidney Disease (KDIGO) (Stage 3b)"
+    disease_classification: "chronic_kidney_disease_kdigo"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "ckd_kdigo_4"
+    name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 4)"
+    name_en: "Chronic Kidney Disease (KDIGO) (Stage 4)"
+    disease_classification: "chronic_kidney_disease_kdigo"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "ckd_kdigo_5"
+    name_de: "Chronische Nierenerkrankung (KDIGO) (Stadium 5)"
+    name_en: "Chronic Kidney Disease (KDIGO) (Stage 5)"
+    disease_classification: "chronic_kidney_disease_kdigo"

endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "khk_1_ge"
+    name_de: "Koronare Gefäßerkrankung (1-Gefäß-Erkrankung)"
+    name_en: "Coronary Vessel Disease (1-Vessel Disease)"
+    disease_classification: "coronary_artery_disease_base_classification"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "khk_2_ge"
+    name_de: "Koronare Gefäßerkrankung (2-Gefäß-Erkrankung)"
+    name_en: "Coronary Vessel Disease (2-Vessel Disease)"
+    disease_classification: "coronary_artery_disease_base_classification"
+
+- model: endoreg_db.disease_classification_choice
+  fields:
+    name: "khk_3_ge"
+    name_de: "Koronare Gefäßerkrankung (3-Gefäß-Erkrankung)"
+    name_en: "Coronary Vessel Disease (3-Vessel Disease)"
+    disease_classification: "coronary_artery_disease_base_classification"

endoreg_db/data/distribution/date/patient.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.date_value_distribution
+  fields:
+    name: "age-screening_colo_population"
+    distribution_type: "uniform"
+    mode: "timedelta"
+    timedelta_days_min: 18250
+    timedelta_days_max: 32485

endoreg_db/data/distribution/numeric/data.yaml

@@ -0,0 +1,14 @@
+- model: endoreg_db.numeric_value_distribution
+  fields:
+    name: "uniform_default"
+    distribution_type: "uniform"
+    min_descriptor: "min_x_1"
+    max_descriptor: "max_x_1"
+
+
+- model: endoreg_db.numeric_value_distribution
+  fields:
+    name: "uniform_high_x1.5"
+    distribution_type: "uniform"
+    min_descriptor: "min_x_1"
+    max_descriptor: "max_x_1.5"

endoreg_db/data/distribution/single_categorical/patient.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.single_categorical_value_distribution
+  fields:
+    name: "gender_random"
+    categories: {
+      "male": 0.5,
+      "female": 0.5
+    }