endoreg-db 0.5.2__py3-none-any.whl → 0.6.0__py3-none-any.whl

endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml

@@ -1,167 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-sodium-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "sodium",
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-# potassium
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-potassium-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "potassium",
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-hemoglobin-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "hemoglobin",
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-# hematocrit
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-hematocrit-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "hematocrit",
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-# platelet count
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-platelets-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "platelets",
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-# white cell count
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-white_blood_cells-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "white_blood_cells",
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-# estimated glomerular filtration rate
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient_lab_sample-add_value-egfr-default"
-    rule_type: "create-object"
-    parent_model: "PatientLabSample"
-    parent_field: "sample"
-    target_model: "PatientLabValue"
-    extra_parameters: {
-      "create_method": {
-          "name": "create_lab_value_by_sample",
-          "kwargs": {
-            "lab_value_name": "estimated_glomerular_filtration_rate", 
-          }
-        },
-        "actions": [
-          {
-            "name": "set_value_by_distribution",
-            "kwargs": {} 
-          }
-        ]
-  
-      }
-
-

endoreg_db/data/case_template/rule/01_patient-set-age.yaml

@@ -1,8 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient-set-age-screening_colo_population"
-    rule_type: "set-field-by_distribution"
-    parent_model: "Patient"
-    target_field: "dob"
-    value_type: "date"
-    date_value_distribution: "age-screening_colo_population"

endoreg_db/data/case_template/rule/01_patient-set-gender.yaml

@@ -1,9 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "patient-set-gender-random"
-    rule_type: "set-field-by_distribution"
-    parent_model: "Patient"
-    target_field: "gender"
-    target_model: "Gender"
-    value_type: "foreign_key"
-    single_categorical_value_distribution: "gender-random"

endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml

@@ -1,23 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "create-patient_lab_sample-default"
-    rule_type: "create-object"
-    target_model: "PatientLabSample"
-    parent_field: "patient"
-    chained_rules: [
-      "patient_lab_sample-add_value-sodium-default",
-      "patient_lab_sample-add_value-potassium-default",
-      "patient_lab_sample-add_value-egfr-default",
-      "patient_lab_sample-add_value-hemoglobin-default",
-      "patient_lab_sample-add_value-hematocrit-default",
-      "patient_lab_sample-add_value-platelets-default",
-      "patient_lab_sample-add_value-white_blood_cells-default"
-    ]
-    extra_parameters: {
-      "create_method": {
-        "name": "create_by_patient",
-        "kwargs": {
-          "sample_type": "generic"
-        }
-      }
-    }

endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml

@@ -1,19 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "create-patient_medication_schedule-anticoagulation-non_valvular_af"
-    rule_type: "create-object"
-    target_model: "PatientMedication"
-    parent_field: "patient"
-
-    chained_rules: [
-
-    ]
-    
-    extra_parameters: {
-      "create_method": {
-        "name": "create_by_patient_and_indication_type",
-        "kwargs": {
-          "indication_type": "thromboembolism-prevention-non_valvular_af"
-        }
-      }
-    }

endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml

@@ -1,19 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "create-patient_medication_schedule-anticoagulation-non_valvular_af"
-    rule_type: "create-object"
-    target_model: "PatientMedicationSchedule"
-    parent_field: "patient"
-
-    chained_rules: [
-
-    ]
-    
-    extra_parameters: {
-      "create_method": {
-        "name": "create_by_patient_and_indication_type",
-        "kwargs": {
-          "indication_type": "thromboembolism-prevention-non_valvular_af"
-        }
-      }
-    }

endoreg_db/data/case_template/rule/19_create_patient.yaml

@@ -1,17 +0,0 @@
-- model: endoreg_db.case_template_rule
-  fields:
-    name: "create-patient-default"
-    rule_type: "create-object"
-    target_model: "Patient"
-    chained_rules: [
-      "patient-set-age-screening_colo_population",
-      "create-patient_lab_sample-default"
-    ]
-    extra_parameters: {
-      "create_method": {
-        "name": "create_generic",
-        "kwargs": {
-          "center": "gplay_case_generator",
-         }
-        }
-    }

endoreg_db/data/case_template/rule_type/base_types.yaml

@@ -1,35 +0,0 @@
-- model: endoreg_db.case_template_rule_type
-  fields:
-    name: "set-field-default"
-    name_de: "Default Wert eines Feldes setzen"
-    name_en: "Set value of field"
-
-- model: endoreg_db.case_template_rule_type
-  fields:
-    name: "set-field-by_distribution"
-    name_de: "Wert eines Feldes anhand einer Verteilung setzen"
-    name_en: "Set value of field by distribution"
-
-- model: endoreg_db.case_template_rule_type
-  fields:
-    name: "set-field-by_value"
-    name_de: "Wert eines Feldes auf einen bestimmten Wert setzen"
-    name_en: "Set value of field to a specific value"
-
-- model: endoreg_db.case_template_rule_type
-  fields:
-    name: "set-field-single_choice"
-    name_de: "Wert eines Feldes auf einen bestimmten Wert anhand einer Auswahl setzen"
-    name_en: "Set value of field to a specific value based on a choice"
-
-- model: endoreg_db.case_template_rule_type
-  fields:
-    name: "set-field-multiple_choice"
-    name_de: "Wert eines Feldes auf einen bestimmten Wert anhand einer Mehrfachauswahl setzen"
-    name_en: "Set value of field to a specific value based on a multiple choice"
-
-- model: endoreg_db.case_template_rule_type
-  fields:
-    name: "create-object"
-    name_de: "Datenbank Objekt erstellen"
-    name_en: "Create Db Object"

endoreg_db/data/case_template/rule_value_type/base_types.yaml

@@ -1,59 +0,0 @@
-- 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

@@ -1,8 +0,0 @@
-- 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

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

endoreg_db/data/case_template/tmp/_rule_value

@@ -1,13 +0,0 @@
-- 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

@@ -1,21 +0,0 @@
-
-- 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

@@ -1,10 +0,0 @@
-- 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

@@ -1,7 +0,0 @@
-- 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

@@ -1,60 +0,0 @@
-# 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"
-    ]
-    last_names: [
-      "Kozielski",
-      "Reiter",
-      "Purrer",
-      "Kudlich",
-      "Brand",
-      "Weich",
-      "Lux",
-      "Meining",
-      "Hann",
-      "Retzbach",
-      "Hose",
-      "Henniger",
-      "Weich",
-      "Dela Cruz",
-      "Wiesemann",
-      "Weise",
-      "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: []
-
-- model: endoreg_db.center
-  fields:
-    name: "gplay_case_generator"
-    name_de: "GPlay Case Generator"
-    name_en: "GPlay Case Generator"
-    first_names: []
-    last_names: []

endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml

@@ -1,144 +0,0 @@
-- 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