endoreg-db 0.8.6.4__py3-none-any.whl

endoreg_db/data/requirement_operator/model_operators.yaml

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+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_all"
+    name_de: "Modelle existieren"
+    name_en: "Models exist"
+    description: "Make sure that all the provided Foreign Key models exist."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_any"
+    name_de: "Mindestens ein Modell existiert"
+    name_en: "At least one model exists"
+    description: "Make sure that at least one of the provided Foreign Key models exist."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_none"
+    name_de: "Kein Modell existiert"
+    name_en: "No model exists"
+    description: "Make sure that none of the provided Foreign Key models exist."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n"
+    name_de: " Exakt n Modelle existieren"
+    name_en: "Exactly n models exist"
+    description: "Make sure that exactly n of the provided Foreign Key models exist. The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_more"
+    name_de: "Mindestens n Modelle existieren"
+    name_en: "At least n models exist"
+    description: "Make sure that at least n of the provided Foreign Key models exist. The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_less"
+    name_de: "Höchstens n Modelle existieren"
+    name_en: "At most n models exist"
+    description: "Make sure that at most n of the provided Foreign Key models exist. The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_count_in_range"
+    name_de: "Anzahl der Modelle liegt im angegebenen Bereich"
+    name_en: "Number of models is in the given range"
+    description: "Make sure that the number of provided Foreign Key models is in the given range. The range is defined using numeric_value_min and numeric_value_max."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_any_in_timeframe"
+    name_de: "Mindestens ein Modell existiert im angegebenen Zeitraum"
+    name_en: "At least one model exists in the given timeframe"
+    description: "Make sure that at least one of the provided Foreign Key models exist and its associated date falls within the specified timeframe. Timeframe is defined by numeric_value_min, numeric_value_max, and unit on the Requirement."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_all_in_timeframe"
+    name_de: "Modelle existieren im angegebenen Zeitraum"
+    name_en: "Models exist in the given timeframe"
+    description: "Make sure that all the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week)."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_none_in_timeframe"
+    name_de: "Kein Modell existiert im angegebenen Zeitraum"
+    name_en: "No model exists in the given timeframe"
+    description: "Make sure that none of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week)."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_in_timeframe"
+    name_de: "Exakt n Modelle existieren im angegebenen Zeitraum"
+    name_en: "Exactly n models exist in the given timeframe"
+    description: "Make sure that exactly n of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week). The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_more_in_timeframe"
+    name_de: "Mindestens n Modelle existieren im angegebenen Zeitraum"
+    name_en: "At least n models exist in the given timeframe"
+    description: "Make sure that at least n of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week). The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_less_in_timeframe"
+    name_de: "Höchstens n Modelle existieren im angegebenen Zeitraum"
+    name_en: "At most n models exist in the given timeframe"
+    description: "Make sure that at most n of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week). The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "patient_medication_schedule_matches_template"
+    description: "Checks if any PatientMedication in the input PatientMedicationSchedule matches the profile (medication, dose, unit, intake times) of any MedicationSchedule template linked to the requirement."
+    evaluation_function_name: "_evaluate_patient_medication_schedule_matches_template"

endoreg_db/data/requirement_set/01_endoscopy_generic.yaml

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+- models: endoreg_db.requirement_set
+  fields:
+    name: "patient_gender_generic"
+    name_de: "Patientengeschlecht (männlich/weiblich)"
+    name_en: "Patient gender generic" 
+    description: "Patient gender (generic)"
+    requirement_set_type: "any"
+    requirements:
+      - patient_gender_is_male
+      - patient_gender_is_female
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "basic_lab_values_normal"
+    name_de: "Basis-Labortests (Unauffällig)"
+    name_en: "Basic Lab Tests (Normal)"
+    description: "Basic lab tests (normal)"
+    requirement_set_type: "all"
+    requirements:
+      - "lab_value_hb_normal"
+      - "lab_value_leukocytes_normal"
+      - "lab_value_platelets_normal"
+      - "lab_value_creatinine_normal"
+      - "lab_value_inr_normal"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "patient_age_generic"
+    name_de: "Patientenalter (18-100 Jahre)"
+    name_en: "Patient Age (18-100 years)"
+    description: "Patient age between 18 and 100 years"
+    requirement_set_type: "all"
+    requirements:
+      - "patient_age_gte_18"
+      - "patient_age_lte_100"
+
+# - models: endoreg_db.requirement_set
+- models: endoreg_db.requirement_set
+  fields:
+    name: "generic_patient"
+    requirement_set_type: "all"
+    description: "Generic patient requirement set"
+    name_de: "Generische Patientenanforderung"
+    name_en: "Generic Patient Requirement"
+    links_to_sets:
+      - "patient_age_generic"
+      - "patient_gender_generic"
+      - "basic_lab_values_normal"

endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml

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+
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_finding_polyp_required_classifications"
+    name_de: "Vorsorge Koloskopie Österreich: Polyp"
+    requirement_set_type: "all"
+    links_to_sets: []
+    requirements:
+      - "colon_austria_screening_polyp_size"
+      - "colonoscopy_austria_screening_polyp_location"
+      - "colonoscopy_austria_screening_polyp_histology"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_examination_complete"
+    requirement_set_type: "any"
+    requirements:
+      - "colonoscopy_austria_screening_examination_cecum_visualized"
+      - "colonoscopy_austria_screening_examination_reason_incomplete"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_examination_required_findings"
+    links_to_sets:
+      - "colonoscopy_austria_screening_examination_complete"
+    requirement_set_type: "all"
+    requirements:
+      - "colonoscopy_austria_screening_bowel_prep"
+      - "colonoscopy_austria_screening_sedation"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_required_patient_information"
+    name_de: "Vorsorge Koloskopie Österreich: Patienteninformation"
+    requirement_set_type: "all"
+    links_to_sets:
+      - "patient_gender_generic"
+      - "patient_age_generic"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_qa"
+    name_de: "Vorsorge Koloskopie Österreich QA"
+    name_en: "Colonoscopy Austria Screening QA"
+    description: "Colonoscopy Austria Screening QA"
+    requirement_set_type: "all"
+    links_to_sets:
+      - "colonoscopy_austria_screening_finding_polyp_required_classifications"
+      - "colonoscopy_austria_screening_required_patient_information"
+      - "colonoscopy_austria_screening_examination_required_findings"
+    tags:
+      - "report_mask_requirement_set"
+      - "colonoscopy_austria_screening"
+    reqset_exam_links:
+      - "colonoscopy_austria_req_sets"
+      - "colonoscopy_req_sets"

endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml

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+- models: endoreg_db.requirement_set
+  fields:
+    name: "endoscopy_bleeding_risk_high"
+    name_de: "Endoskopie - Blutungsrisiko: hoch"
+    name_en: "Endoscopy - Bleeding Risk: High"
+    description: "Endoskopie - Blutungsrisiko: hoch"
+    # linked_sets: [] # if this rule depends on others
+    requirement_set_type: "any"
+    requirements:
+      - "endoscopy_intervention_bleeding_risk_high"
+
+
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "endoscopy_bleeding_risk_low"
+    name_de: "Endoskopie - Blutungsrisiko: niedrig"
+    name_en: "Endoscopy - Bleeding Risk: Low"
+    description: "Endoskopie - Blutungsrisiko: niedrig"
+    # linked_sets: [] # if this rule depends on others
+    requirement_set_type: "any"
+    requirements:
+      - "endoscopy_intervention_bleeding_risk_low"
+    links_to_sets: []
+
+
+
+    
+- models: endoreg_db.requirement_set
+  fields:
+    name: "patient_medication_indication_anticoagulation"
+    name_de: "Patientenmedikation - Antikoagulation"
+    name_en: "Patient Medication - Anticoagulation"
+    description: "Patient medication - anticoagulation"
+    requirement_set_type: "any"
+    requirements:
+      - "indication_non_valvular_af_apixaban_is_defined_in_requirement"
+      - "indication_after_hip_apixaban_is_defined_in_requirement"
+      - "indication_after_knee_apixaban_is_defined_in_requirement"
+    
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "high_bleed_risk_endoscopy_w_patient_w_anticoagulation"
+    name_de: "Endoskopie - hohes Blutungsrisiko mit generischen Patientenanforderungen"
+    name_en: "High Bleed Risk Endoscopy with Generic Patient Requirements"
+    description: "High bleed risk endoscopy with generic patient requirements"
+    requirement_set_type: "all"
+    links_to_sets:
+      - "endoscopy_bleeding_risk_high"
+      - "generic_patient"
+      - "patient_medication_indication_anticoagulation"

endoreg_db/data/requirement_set_type/data.yaml

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+- model: endoreg_db.requirement_set_type
+  fields:
+    name: "all"
+    name_de: "alle"
+    name_en: "all"
+    description: "All requirement are true"
+
+- model: endoreg_db.requirement_set_type
+  fields:
+    name: "any"
+    name_de: "mindestens eine"
+    name_en: "at least one"
+    description: "At least one requirement is true"
+
+- model: endoreg_db.requirement_set_type
+  fields:
+    name: "none"
+    name_de: "keine"
+    name_en: "none"
+    description: "No requirement is true"

endoreg_db/data/requirement_type/requirement_types.yaml

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+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_examination"
+    name_de: "Patientenuntersuchung"
+    name_en: "Patient examination"
+    description: "Requirements of this type are used on PatientExamination Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_lab_sample"
+    name_de: "Patientenlabormuster"
+    name_en: "Patient lab sample"
+    description: "Requirements of this type are used on PatientLabSample Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_lab_value"
+    name_de: "Patientenlaborwert"
+    name_en: "Patient lab value"
+    description: "Requirements of this type are used on PatientLabValue Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_disease"
+    name_de: "Patientenerkrankung"
+    name_en: "Patient Disease"
+    description: "Requirements of this type are used on PatientDisease Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "examination"
+    name_de: "Untersuchung"
+    name_en: "Examination"
+    description: "Examination-related requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "examination_indication"
+    name_de: "Untersuchungsindikation"
+    name_en: "Examination Indication"
+    description: "Examination indication requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "disease"
+    name_de: "Erkrankung"
+    name_en: "Disease"
+    description: "Disease-related requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "disease_classification_choice"
+    name_de: "Erkrankungsklassifikation"
+    name_en: "Disease Classification"
+    description: "Disease classification choice requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "event"
+    name_de: "Ereignis"
+    name_en: "Event"
+    description: "Event-related requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "lab_value"
+    name_de: "Laborwert"
+    name_en: "Lab Value"
+    description: "Lab value requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding"
+    name_de: "Befund"
+    name_en: "Finding"
+    description: "Finding requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_morphology"
+    name_de: "Befundmorphologie"
+    name_en: "Finding Morphology"
+    description: "Finding morphology requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_location"
+    name_de: "Befundlokalisation"
+    name_en: "Finding Location"
+    description: "Finding location requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_intervention"
+    name_de: "Befundintervention"
+    name_en: "Finding Intervention"
+    description: "Finding intervention requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "finding_interventions"
+    name_de: "Befundinterventionen (multiple)"
+    name_en: "Finding Interventions (multiple)"
+    description: "Finding interventions (multiple) requirements"
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient"
+    name_de: "Patient"
+    name_en: "Patient"
+    description: "Relates to a patient record."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_event"
+    name_de: "Patientenereignis"
+    name_en: "Patient Event"
+    description: "Requirements of this type are used on PatientEvent Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_finding"
+    
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_medication"
+    name_de: "Patientenmedikation"
+    name_en: "Patient Medication"
+    description: "Requirements of this type are used on PatientMedication Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "medication"
+    name_de: "Medikament"
+    name_en: "Medication"
+    description: "Requirements of this type are used on Medication Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "medication_indication"
+    name_de: "Medikationsindikation"
+    name_en: "Medication Indication"
+    description: "Requirements of this type are used on MedicationIndication Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "medication_intake_time"
+    name_de: "Medikamenteneinnahmezeit"
+    name_en: "Medication Intake Time"
+    description: "Requirements of this type are used on MedicationIntakeTime Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "medication_schedule"
+    name_de: "Medikationsschema"
+    name_en: "Medication Schedule"
+    description: "Requirements of this type are used on MedicationSchedule Objects."
+
+- model: endoreg_db.requirement_type
+  fields:
+    name: "patient_medication_schedule"
+    name_de: "Patienten-Medikationsplan"
+    name_en: "Patient Medication Schedule"
+    description: "Represents a patient's overall medication schedule, which may contain multiple patient medications."

endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml

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+- fields:
+    name: gas
+    name_de: Erdgas
+    name_en: Gas
+  model: endoreg_db.Resource
+- fields:
+    name: oil
+    name_de: "Heizöl"
+    name_en: Oil
+  model: endoreg_db.Resource
+- fields:
+    name: electricity
+    name_de: Strom
+    name_en: Electricity
+  model: endoreg_db.Resource

endoreg_db/data/risk/bleeding.yaml

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+- model: endoreg_db.risk
+  fields:
+    name: "bleeding_low"
+    name_de: "Blutung (niedrig)"
+    name_en: "Bleeding (low)"
+    description: "Low bleeding risk"
+    risk_type: "bleeding"
+    risk_value: 1
+
+- model: endoreg_db.risk
+  fields:
+    name: "bleeding_high"
+    name_de: "Blutung (hoch)"
+    name_en: "Bleeding (high)"
+    description: "High bleeding risk"
+    risk_type: "bleeding"
+    risk_value: 3
+
+- model: endoreg_db.risk
+  fields:
+    name: "bleeding_unknown"
+    name_de: "Blutung (unbekannt)"
+    name_en: "Bleeding (unknown)"
+    description: "Unknown bleeding risk"
+    risk_type: "bleeding"
+    risk_value: 0

endoreg_db/data/risk/thrombosis.yaml

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+# high medium low thrombosis risk
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_high"
+    name_de: "Thrombose hoch"
+    name_en: "Thrombosis high"
+    description: "High thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 3
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_medium"
+    name_de: "Thrombose mittel"
+    name_en: "Thrombosis medium"
+    description: "Medium thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 2
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_low"
+    name_de: "Thrombose niedrig"
+    name_en: "Thrombosis low"
+    description: "Low thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 1
+
+- model: endoreg_db.risk
+  fields:
+    name: "thrombosis_unknown"
+    name_de: "Thrombose unbekannt"
+    name_en: "Thrombosis unknown"
+    description: "Unknown thrombosis risk"
+    risk_type: "thrombosis"
+    risk_value: 0

endoreg_db/data/risk_type/data.yaml

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+- model: endoreg_db.risk_type
+  fields:
+    name: "bleeding"
+    name_de: "Blutung"
+    name_en: "Bleeding"
+    description: "Bleeding risk"
+
+- model: endoreg_db.risk_type
+  fields:
+    name: "perforation"
+    name_de: "Perforation"
+    name_en: "Perforation"
+    description: "Perforation risk"
+
+- model: endoreg_db.risk_type
+  fields:
+    name: "infection"
+    name_de: "Infektion"
+    name_en: "Infection"
+    description: "Infection risk"
+
+- model: endoreg_db.risk_type
+  fields:
+    name: "thrombosis"
+    name_de: "Thrombose"
+    name_en: "Thrombosis"
+    description: "Thrombosis risk"

endoreg_db/data/setup_config.yaml

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+# EndoReg DB Setup Configuration
+# This file defines which models should be used for setup and their fallback configurations
+
+default_models:
+  primary_classification_model: "image_multilabel_classification_colonoscopy_default"
+  primary_labelset: "multilabel_classification_colonoscopy_default"
+
+# HuggingFace fallback configuration
+huggingface_fallback:
+  enabled: true
+  repo_id: "wg-lux/colo_segmentation_RegNetX800MF_base"
+  filename: "colo_segmentation_RegNetX800MF_base.ckpt"
+  labelset_name: "multilabel_classification_colonoscopy_default"
+
+# Local weights search patterns
+weights_search_patterns:
+  # Primary model weight filename patterns (supports wildcards)
+  - "colo_segmentation_RegNetX800MF_*.ckpt"
+  - "image_multilabel_classification_colonoscopy_default_*.ckpt"
+  - "*_colonoscopy_*.ckpt"
+
+# Search directories for local weights (relative to project root)
+weights_search_dirs:
+  - "tests/assets"
+  - "assets"
+  - "data/storage/model_weights"
+  - "${STORAGE_DIR}/model_weights" # Environment variable substitution
+
+# Auto-generation defaults when creating metadata
+auto_generation_defaults:
+  activation: "sigmoid"
+  mean: "0.485,0.456,0.406" # ImageNet defaults
+  std: "0.229,0.224,0.225" # ImageNet defaults
+  size_x: 224
+  size_y: 224
+  axes: "CHW"
+  batchsize: 32
+  num_workers: 4

endoreg_db/data/shift/endoscopy.yaml

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+- model: endoreg_db.shift
+  fields:
+    name: "endoscopy_base"
+    name_de: "Endoskopie (Basis)"
+    name_en: "Endoscopy (Base)"
+    description: "This shift represents a basic, planned endoscopy shift (EGD, colonoscopy)."
+    required_qualifications: 
+      - "endoscopy_base"
+    shift_types:
+    
+
+- model: endoreg_db.shift
+  fields:
+    name: "endoscopy_training"
+    name_de: "Endoskopie (Training)"
+    name_en: "Endoscopy (Training)"
+    description: "This shift represents a training endoscopy shift which is covered 1:1 with an experienced endoscopist."
+    required_qualifications: 
+      - "endoscopy_supervised"
+
+

endoreg_db/data/shift_type/base.yaml

@@ -0,0 +1,35 @@
+- model: endoreg_db.shift_type
+  fields:
+    name: "regular"
+    name_de: "Regulär"
+    name_en: "Regular"
+
+- model: endoreg_db.shift_type
+  fields:
+    name: "supervision"
+    name_de: "Supervision"
+    name_en: "Supervision"
+
+- model: endoreg_db.shift_type
+  fields:
+    name: "off_hours"
+    name_de: "Nicht reguläre Arbeitszeit ('Dienste')"
+    name_en: "Off Hours"
+
+- model: endoreg_db.shift_type
+  fields:
+    name: "on_call"
+    name_de: "Bereitschaftsdienst"
+    name_en: "On Call"
+
+- model: endoreg_db.shift_type
+  fields:
+    name: "ward"
+    name_de: "Station"
+    name_en: "Ward"
+
+- model: endoreg_db.shift_type
+  fields:
+    name: "miscellaneous"
+    name_de: "Sonstiges"
+    name_en: "Miscellaneous"

endoreg_db/data/tag/requirement_set_tags.yaml

@@ -0,0 +1,11 @@
+- model: endoreg_db.tag
+  fields:
+    name: "report_mask_requirement_set"
+
+- model: endoreg_db.tag
+  fields:
+    name: "colonoscopy_austria_screening"
+
+- model: endoreg_db.tag
+  fields:
+    name: "colonoscopy_austria"

endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml

@@ -0,0 +1,12 @@
+- fields:
+    distance: 1000
+    emission_factor: transport_product_emission_generic_europe
+    name: generic_europe
+    unit: kilometer
+  model: endoreg_db.TransportRoute
+- fields:
+    distance: 10000
+    emission_factor: transport_product_emission_generic_overseas
+    name: generic_overseas
+    unit: kilometer
+  model: endoreg_db.TransportRoute