endoreg-db 0.8.9.32__py3-none-any.whl

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.safetensors"
+  labelset_name: "multilabel_classification_colonoscopy_default"
+
+# Local weights search patterns
+weights_search_patterns:
+  # Primary model weight filename patterns (supports wildcards)
+  - "colo_segmentation_RegNetX800MF_*.safetensors"
+  - "image_multilabel_classification_colonoscopy_default_*.safetensors"
+  - "*_colonoscopy_*.safetensors"
+
+# 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

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+- 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

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+- 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"
+
+# User role tags for requirement set filtering
+- model: endoreg_db.tag
+  fields:
+    name: "Gastroenterologist"
+
+- model: endoreg_db.tag
+  fields:
+    name: "Student"
+
+- model: endoreg_db.tag
+  fields:
+    name: "Professor"
+
+- model: endoreg_db.tag
+  fields:
+    name: "Terminology Expert"
+
+- model: endoreg_db.tag
+  fields:
+    name: "Default Prototype"

endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml

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+- 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

endoreg_db/data/unit/concentration.yaml

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+# g / l and equivalents; ascending by gram, then ascending by liter
+- model: endoreg_db.unit
+  fields: 
+    name: "picogram per mililiter"
+    name_de: "Pikogramm pro Mililiter"
+    name_en: "picogram per mililiter"
+    abbreviation: "pg/ml"
+
+# gram per liter
+- model: endoreg_db.unit
+  fields:
+    name: "gram per liter"
+    name_de: "Gramm pro Liter"
+    name_en: "gram per liter"
+    abbreviation: "g/L"
+
+# micromole per liter: 
+- model: endoreg_db.unit
+  fields:
+    name: "micromole per liter"
+    name_de: "Mikromol pro Liter"
+    name_en: "micromole per liter"
+    abbreviation: "µmol/L"
+
+- model: endoreg_db.unit
+  fields:
+    name: "nanogram per mililiter"
+    name_de: "Nanogramm pro Mililiter"
+    name_en: "nanogram per mililiter"
+    abbreviation: "ng/ml"
+
+- model: endoreg_db.unit
+  fields:
+    name: "nanogram per deciliter"
+    name_de: "Nanogramm pro Deziliter"
+    name_en: "nanogram per deciliter"
+
+- model: endoreg_db.unit
+  fields:
+    name: "microgram per mililiter"
+    name_de: "Microgramm pro Mililiter"
+    name_en: "microgram per mililiter"
+    abbreviation: "µg/ml"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "microgram per deciliter"
+    abbreviation: "µg/dL"
+    name_de: "Mikrogramm pro Deziliter"
+    name_en: "microgram per deciliter"
+    description: "Micrograms per deciliter, a unit of measurement for concentration."
+
+- model: endoreg_db.unit
+  fields:
+    name: "gram per deciliter"
+    name_de: "Gramm pro Deziliter"
+    name_en: "gram per deciliter"
+  
+
+# mol / l
+- model: endoreg_db.Unit
+  fields:
+    name: "milimole per liter"
+    abbreviation: "mmol/L"
+    name_de: "milimol pro Liter"
+    name_en: "milimole per liter"
+    description: "milimoles per liter, a unit of measurement for concentration in blood."
+
+- model: endoreg_db.Unit
+  fields:
+    name: "miliequivalent per liter"
+    abbreviation: "mEq/L"
+    name_de: "miliäquivalent pro Liter"
+    name_en: "miliequivalent per liter"
+    description: "miliequivalents per liter, used for electrolytes concentration."
+
+- model: endoreg_db.Unit
+  fields:
+    name: "miligram per deciliter"
+    abbreviation: "mg/dL"
+    name_de: "miligramm pro Deziliter"
+    name_en: "miligram per deciliter"
+    description: "miligrams per deciliter, commonly used for various blood measurements."
+
+- model: endoreg_db.Unit
+  fields:
+    name: "miligram per liter"
+    abbreviation: "mg/L"
+    name_de: "miligramm pro Liter"
+    name_en: "miligram per liter"
+    description: "miligrams per liter, a unit of measurement for concentration in blood."
+
+# x 10^9 per liter
+- model: endoreg_db.Unit
+  fields:
+    name: "x 10^9 per liter"
+    abbreviation: "x 10^9/L"
+    name_de: "x 10^9 pro Liter"
+    name_en: "x 10^9 per liter"
+    description: "Number of cells per liter, often used for blood cell counts."
+
+# U / l
+- model: endoreg_db.unit
+  fields:
+    name: "units per liter"
+    name_de: "Units pro Liter"
+    name_en: "units per liter"
+    abbreviation: "U/l"
+
+- model: endoreg_db.unit
+  fields:
+    name: "microinternational units per mililiter"
+    name_de: "Mikro-Internationale Einheiten pro Mililiter"
+    name_en: "micro-international units per mililiter"
+    abbreviation: "µU/ml"

endoreg_db/data/unit/data.yaml

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+- model: endoreg_db.Unit
+  fields:
+    name: "liters-per-minute"
+    abbreviation: "l/min"
+    name_de: "Liter pro Minute"
+    name_en: "Liters per Minute"
+    description: "liters per minute"
+
+
+# kilowatt-hours
+- model: endoreg_db.Unit
+  fields:
+    name: "kilowatt-hours"
+    abbreviation: "kWh"
+    name_de: "Kilowattstunden"
+    name_en: "Kilowatt-hours"
+    description: "kilowatt-hours"

endoreg_db/data/unit/length.yaml

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+- model: endoreg_db.Unit
+  fields:
+    name: "milimeter"
+    abbreviation: "mm"
+    name_de: "milimeter"
+    name_en: "milimeter"
+    description: "milimeters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "centimeter"
+    abbreviation: "cm"
+    name_de: "Zentimeter"
+    name_en: "Centimeter"
+    description: "centimeters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "meter"
+    abbreviation: "m"
+    name_de: "Meter"
+    name_en: "Meter"
+    description: "meters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "kilometer"
+    abbreviation: "km"
+    name_de: "Kilometer"
+    name_en: "Kilometer"
+    description: "kilometers"

endoreg_db/data/unit/misc.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.unit
+  fields:
+    name: "percent"
+    abbreviation: "%"
+    name_de: "Prozent"
+    name_en: "percent"
+
+- model: endoreg_db.unit
+  fields:
+    name: "ratio"
+    abbreviation: ""
+    name_de: "Ratio"
+    name_en: "ratio"
+
+- model: endoreg_db.unit
+  fields:
+    name: "dose"
+    name_de: "Dosierung(en)"
+    name_en: "dose(s)"
+    abbreviation: ""

endoreg_db/data/unit/rate.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.unit
+  fields:
+    name: "mililiter per minute per 1.73m^2"
+    name_de: "ml/min/1.73m²"
+    name_en: "ml/min/1.73m²"
+    abbreviation: "ml/min/1.73m²"

endoreg_db/data/unit/time.yaml

@@ -0,0 +1,48 @@
+- model: endoreg_db.unit
+  fields:
+    name: "seconds"
+    abbreviation: "s"
+    name_de: "Sekunden"
+    name_en: "Sekunden"
+
+- model: endoreg_db.unit
+  fields:
+    name: "minutes"
+    abbreviation: "min"
+    name_de: "Minuten"
+    name_en: "Minutes"
+
+- model: endoreg_db.unit
+  fields:
+    name: "hours"
+    abbreviation: "h"
+    name_de: "Stunden"
+    name_en: "Hours"
+
+- model: endoreg_db.unit
+  fields:
+    name: "days"
+    abbreviation: "d"
+    name_de: "Tage"
+    name_en: "Days"
+
+- model: endoreg_db.unit
+  fields:
+    name: "weeks"
+    abbreviation: "w"
+    name_de: "Wochen"
+    name_en: "Weeks"
+
+- model: endoreg_db.unit
+  fields:
+    name: "months"
+    abbreviation: "mo"
+    name_de: "Monate"
+    name_en: "Months"
+
+- model: endoreg_db.unit
+  fields:
+    name: "years"
+    abbreviation: "y"
+    name_de: "Jahre"
+    name_en: "Years"