feature:
Full SOFA Score: Data Layer + Scoring Engine Glasgow Coma Scale: Data Layer + Scoring Engine
This commit is contained in:
voltsrage
@@ -0,0 +1,160 @@
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public static class SofaCalculator
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{
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public static readonly IReadOnlyList<string> SofaObservationCodes = new[]
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{
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"PAO2_MMHG", "FIO2_PCT", "PLATELET_K_UL", "BILIRUBIN_MG_DL",
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"CREATININE_MG_DL", "URINE_OUTPUT_ML_H",
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"SYSTOLIC_BP", "DIASTOLIC_BP", "SPO2", "SUPPLEMENTAL_O2"
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};
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public static readonly IReadOnlySet<string> SofaCodeSet =
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new HashSet<string>(SofaObservationCodes);
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public static bool IsSofaCode(string observationCode) =>
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SofaCodeSet.Contains(observationCode);
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// GCS components and gcs.scored also trigger SOFA re-score (CNS organ system)
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public static bool TriggersRescore(string observationCode) =>
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IsSofaCode(observationCode) || GcsCalculator.IsGcsCode(observationCode);
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public static string CacheKey(Guid encounterId, string code) =>
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$"sofa:{encounterId}:{code}";
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// --- 1. Respiratory: PaO2/FiO2 ratio ---
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public static int ScoreRespiratory(decimal? pao2, decimal? fio2, bool onMechanicalVent)
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{
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if (pao2 is null || fio2 is null || fio2 == 0) return 0;
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var ratio = pao2.Value / (fio2.Value / 100m);
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return ratio switch
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{
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>= 400 when onMechanicalVent => 0,
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>= 400 => 0,
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>= 300 => 1,
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>= 200 => 2,
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>= 100 when onMechanicalVent => 3,
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>= 100 => 2,
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_ when onMechanicalVent => 4,
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_ => 3
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};
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}
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// SpO2/FiO2 proxy when PaO2 unavailable (Rice et al. 2007)
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public static int ScoreRespiratoryFromSpo2(decimal? spo2, decimal? fio2, bool onMechanicalVent)
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{
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if (spo2 is null || fio2 is null || fio2 == 0) return 0;
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var sfRatio = spo2.Value / (fio2.Value / 100m);
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return sfRatio switch
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{
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>= 315 => 0,
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>= 235 => 1,
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>= 150 => 2,
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>= 67 when onMechanicalVent => 3,
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>= 67 => 2,
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_ when onMechanicalVent => 4,
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_ => 3
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};
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}
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// --- 2. Coagulation: Platelet count (k/µL) ---
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public static int ScoreCoagulation(decimal? platelets)
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{
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if (platelets is null) return 0;
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return platelets.Value switch
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{
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>= 150 => 0,
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>= 100 => 1,
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>= 50 => 2,
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>= 20 => 3,
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_ => 4
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};
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}
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// --- 3. Liver: Bilirubin (mg/dL) ---
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public static int ScoreLiver(decimal? bilirubin)
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{
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if (bilirubin is null) return 0;
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return bilirubin.Value switch
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{
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< 1.2m => 0,
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< 2.0m => 1,
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< 6.0m => 2,
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< 12.0m => 3,
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_ => 4
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};
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}
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// --- 4. Cardiovascular: MAP and vasopressor dose ---
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public static int ScoreCardiovascular(decimal? map, VasopressorInfo? vasopressor)
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{
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if (vasopressor is not null)
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{
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return vasopressor.DrugName.ToUpperInvariant() switch
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{
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"DOPAMINE" when vasopressor.DoseUgKgMin > 15m => 4,
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"EPINEPHRINE" when vasopressor.DoseUgKgMin > 0.1m => 4,
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"NOREPINEPHRINE" when vasopressor.DoseUgKgMin > 0.1m => 4,
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"DOPAMINE" when vasopressor.DoseUgKgMin > 5m => 3,
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"EPINEPHRINE" => 3,
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"NOREPINEPHRINE" => 3,
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"DOPAMINE" => 2,
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"DOBUTAMINE" => 2,
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_ => 1
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};
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}
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if (map is null) return 0;
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return map.Value < 70m ? 1 : 0;
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}
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// --- 5. CNS: Glasgow Coma Scale (from Phase 25) ---
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public static int ScoreCns(int? gcsTotal) =>
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GcsCalculator.ToSofaCnsScore(gcsTotal ?? 15);
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// --- 6. Renal: Creatinine (mg/dL) or urine output (mL/day) ---
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public static int ScoreRenal(decimal? creatinine, decimal? urineOutputMlPerDay)
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{
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var creatScore = creatinine switch
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{
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null => 0,
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< 1.2m => 0,
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< 2.0m => 1,
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< 3.5m => 2,
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< 5.0m => 3,
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_ => 4
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};
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var urineScore = urineOutputMlPerDay switch
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{
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null => 0,
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< 200m => 4,
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< 500m => 3,
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_ => 0
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};
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return Math.Max(creatScore, urineScore);
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}
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public static SofaResult ComputeTotal(
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int respiratory, int coagulation, int liver,
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int cardiovascular, int cns, int renal) =>
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new(
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Total: respiratory + coagulation + liver + cardiovascular + cns + renal,
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Respiratory: respiratory,
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Coagulation: coagulation,
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Liver: liver,
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Cardiovascular: cardiovascular,
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Cns: cns,
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Renal: renal);
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// Count organ systems with component data for baseline eligibility
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public static int CountPopulatedOrganSystems(
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bool hasRespiratory,
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bool hasCoagulation,
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bool hasLiver,
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bool hasCardiovascular,
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bool hasCns,
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bool hasRenal) =>
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new[] { hasRespiratory, hasCoagulation, hasLiver,
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hasCardiovascular, hasCns, hasRenal }
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.Count(hasData => hasData);
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}
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@@ -0,0 +1,340 @@
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using System.Globalization;
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using System.Text.Json;
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using Microsoft.EntityFrameworkCore;
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using Microsoft.Extensions.Options;
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using Prometheus;
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using StackExchange.Redis;
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public class SofaDetector
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{
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private static readonly JsonSerializerOptions JsonOptions = new()
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{
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PropertyNameCaseInsensitive = true
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};
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private readonly IConnectionMultiplexer _redis;
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private readonly IServiceProvider _services;
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private readonly SofaLabCache _labCache;
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private readonly SofaVasopressorResolver _vasopressors;
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private readonly SofaOptions _options;
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private readonly ClinicalMetrics _metrics;
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private readonly ILogger<SofaDetector> _logger;
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public SofaDetector(
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IConnectionMultiplexer redis,
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IServiceProvider services,
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SofaLabCache labCache,
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SofaVasopressorResolver vasopressors,
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IOptions<SofaOptions> options,
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ClinicalMetrics metrics,
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ILogger<SofaDetector> logger)
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{
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_redis = redis;
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_services = services;
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_labCache = labCache;
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_vasopressors = vasopressors;
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_options = options.Value;
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_metrics = metrics;
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_logger = logger;
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}
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public async Task<SofaScoringResult> ProcessObservationAsync(
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Guid encounterId,
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Guid patientId,
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string observationCode,
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decimal value,
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DateTimeOffset recordedAt,
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CancellationToken ct = default)
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{
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if (!SofaCalculator.TriggersRescore(observationCode))
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return SofaScoringResult.NotSofaTrigger;
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if (SofaCalculator.IsSofaCode(observationCode))
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{
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await _labCache.StoreAsync(encounterId, observationCode, value, recordedAt);
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}
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return await TryComputeScoreAsync(encounterId, patientId, ct);
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}
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public Task<SofaScoringResult> ProcessGcsScoredAsync(
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Guid encounterId, Guid patientId, CancellationToken ct = default) =>
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TryComputeScoreAsync(encounterId, patientId, ct);
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private async Task<SofaScoringResult> TryComputeScoreAsync(
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Guid encounterId, Guid patientId, CancellationToken ct)
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{
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using var timer = _metrics.SofaScoringDuration.NewTimer();
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using (var scope = _services.CreateScope())
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{
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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if (!await db.Encounters.AnyAsync(e => e.Id == encounterId, ct))
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{
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_logger.LogWarning(
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"Skipping SOFA score for unknown encounter {EncounterId}", encounterId);
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return SofaScoringResult.EncounterNotFound;
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}
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}
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var cached = await _labCache.GetAllAsync(encounterId);
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var staleComponents = new List<string>();
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var missingComponents = new List<string>();
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decimal? GetValue(string code)
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{
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if (!cached.TryGetValue(code, out var entry))
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{
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missingComponents.Add(code);
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return null;
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}
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var status = _labCache.Classify(entry);
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if (status == SofaValueStatus.Expired)
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{
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missingComponents.Add(code);
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return null;
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}
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if (status == SofaValueStatus.Stale)
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staleComponents.Add(code);
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return entry.Value;
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}
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var pao2 = GetValue("PAO2_MMHG");
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var fio2 = GetValue("FIO2_PCT");
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var spo2 = GetValue("SPO2");
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var supplementalO2 = GetValue("SUPPLEMENTAL_O2");
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var onMechanicalVent = supplementalO2 is >= 1m;
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var usedSpO2Fallback = false;
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int respiratory;
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if (pao2 is not null && fio2 is not null)
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{
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respiratory = SofaCalculator.ScoreRespiratory(pao2, fio2, onMechanicalVent);
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}
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else if (_options.UseSpO2FiO2Fallback && spo2 is not null && fio2 is not null)
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{
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usedSpO2Fallback = true;
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respiratory = SofaCalculator.ScoreRespiratoryFromSpo2(spo2, fio2, onMechanicalVent);
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}
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else
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{
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respiratory = 0;
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if (pao2 is null) missingComponents.Add("PAO2_MMHG");
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if (fio2 is null) missingComponents.Add("FIO2_PCT");
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}
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var coagulation = SofaCalculator.ScoreCoagulation(GetValue("PLATELET_K_UL"));
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var liver = SofaCalculator.ScoreLiver(GetValue("BILIRUBIN_MG_DL"));
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decimal? map = null;
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var sbp = GetValue("SYSTOLIC_BP");
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var dbp = GetValue("DIASTOLIC_BP");
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if (sbp is not null && dbp is not null)
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map = MapCalculator.Calculate(sbp.Value, dbp.Value);
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var vasopressor = await _vasopressors.GetActiveVasopressorAsync(encounterId, ct);
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var cardiovascular = SofaCalculator.ScoreCardiovascular(map, vasopressor);
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var gcsTotal = await LoadGcsTotalAsync(encounterId);
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var cns = SofaCalculator.ScoreCns(gcsTotal);
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var creatinine = GetValue("CREATININE_MG_DL");
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var urineMlH = GetValue("URINE_OUTPUT_ML_H");
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decimal? urineMlDay = urineMlH is not null ? urineMlH * 24m : null;
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var renal = SofaCalculator.ScoreRenal(creatinine, urineMlDay);
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var result = SofaCalculator.ComputeTotal(
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respiratory, coagulation, liver, cardiovascular, cns, renal);
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var stalenessFlags = JsonSerializer.Serialize(new SofaStalenessFlags(
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staleComponents.Distinct().ToList(),
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missingComponents.Distinct().ToList(),
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usedSpO2Fallback), JsonOptions);
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var calculatedAt = DateTimeOffset.UtcNow;
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var (isBaseline, delta) = await ResolveBaselineAndDeltaAsync(
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encounterId, patientId, result, calculatedAt,
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SofaCalculator.CountPopulatedOrganSystems(
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hasRespiratory: (pao2 is not null && fio2 is not null)
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|| (_options.UseSpO2FiO2Fallback && spo2 is not null && fio2 is not null),
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hasCoagulation: cached.ContainsKey("PLATELET_K_UL")
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&& _labCache.Classify(cached["PLATELET_K_UL"]) != SofaValueStatus.Expired,
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hasLiver: cached.ContainsKey("BILIRUBIN_MG_DL")
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&& _labCache.Classify(cached["BILIRUBIN_MG_DL"]) != SofaValueStatus.Expired,
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hasCardiovascular: (sbp is not null && dbp is not null) || vasopressor is not null,
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hasCns: gcsTotal is not null,
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hasRenal: (cached.ContainsKey("CREATININE_MG_DL")
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&& _labCache.Classify(cached["CREATININE_MG_DL"]) != SofaValueStatus.Expired)
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|| (cached.ContainsKey("URINE_OUTPUT_ML_H")
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&& _labCache.Classify(cached["URINE_OUTPUT_ML_H"]) != SofaValueStatus.Expired)),
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ct);
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await PersistScoreAsync(
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encounterId, patientId, result, isBaseline, delta,
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stalenessFlags, calculatedAt, ct);
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var alertCreated = false;
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if (delta is >= 2)
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{
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alertCreated = await TryCreateAlertAsync(
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encounterId, patientId, AlertType.SofaSepsis, AlertSeverity.Critical,
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result, isBaseline ? null : delta, stalenessFlags, ct);
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}
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else if (delta == 1)
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{
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alertCreated = await TryCreateAlertAsync(
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encounterId, patientId, AlertType.SofaWarning, AlertSeverity.Warning,
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result, delta, stalenessFlags, ct);
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}
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_metrics.SofaScoresTotal
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.WithLabels(alertCreated ? "true" : "false")
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.Inc();
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_logger.LogInformation(
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"SOFA score {Total} for encounter {Id} — baseline={Baseline} delta={Delta}",
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result.Total, encounterId, isBaseline, delta);
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return new SofaScoringResult(
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SofaOutcome.ScoreComputed, result, isBaseline, delta, alertCreated);
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}
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private async Task<int?> LoadGcsTotalAsync(Guid encounterId)
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{
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var cache = _redis.GetDatabase();
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var gcsValues = await cache.StringGetAsync(GcsCalculator.AllComponentKeys(encounterId));
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if (!gcsValues.All(v => v.HasValue)) return null;
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var eye = decimal.Parse(gcsValues[0]!, CultureInfo.InvariantCulture);
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var verbal = decimal.Parse(gcsValues[1]!, CultureInfo.InvariantCulture);
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var motor = decimal.Parse(gcsValues[2]!, CultureInfo.InvariantCulture);
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return GcsCalculator.ComputeTotal(eye, verbal, motor);
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}
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private async Task<(bool IsBaseline, int? Delta)> ResolveBaselineAndDeltaAsync(
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Guid encounterId, Guid patientId, SofaResult result,
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DateTimeOffset calculatedAt, int populatedOrganSystems, CancellationToken ct)
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{
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using var scope = _services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var existingBaseline = await db.SofaScores
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.AsNoTracking()
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.FirstOrDefaultAsync(s => s.EncounterId == encounterId && s.IsBaseline, ct);
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if (existingBaseline is null)
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{
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if (populatedOrganSystems >= 4)
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return (true, null);
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return (false, null);
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}
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var delta = result.Total - existingBaseline.TotalScore;
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return (false, delta);
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}
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private async Task PersistScoreAsync(
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Guid encounterId, Guid patientId, SofaResult result,
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bool isBaseline, int? delta, string stalenessFlags,
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DateTimeOffset calculatedAt, CancellationToken ct)
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{
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using var scope = _services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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db.SofaScores.Add(new SofaScore
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{
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Id = Guid.NewGuid(),
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EncounterId = encounterId,
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PatientId = patientId,
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TotalScore = result.Total,
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RespiratoryScore = result.Respiratory,
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CoagulationScore = result.Coagulation,
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LiverScore = result.Liver,
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CardiovascularScore = result.Cardiovascular,
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CnsScore = result.Cns,
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RenalScore = result.Renal,
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IsBaseline = isBaseline,
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DeltaFromBaseline = delta,
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StalenessFlags = stalenessFlags,
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CalculatedAt = calculatedAt,
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CreatedAt = DateTimeOffset.UtcNow
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});
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await db.SaveChangesAsync(ct);
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}
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private async Task<bool> TryCreateAlertAsync(
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Guid encounterId, Guid patientId,
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AlertType alertType, AlertSeverity severity,
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SofaResult result, int? delta, string stalenessFlags,
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CancellationToken ct)
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{
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if (alertType == AlertType.SofaWarning)
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{
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var suppression = _services.GetRequiredService<IAlertSuppressionService>();
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if (await suppression.IsSuppressedAsync(encounterId, alertType, ct))
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return false;
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}
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using var scope = _services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await using var tx = await db.Database.BeginTransactionAsync(ct);
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var alertId = Guid.NewGuid();
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var triggeredAt = DateTimeOffset.UtcNow;
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var details =
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$"SOFA score {result.Total} (delta +{delta}). " +
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$"Components: Resp={result.Respiratory}, Coag={result.Coagulation}, " +
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$"Liver={result.Liver}, CV={result.Cardiovascular}, CNS={result.Cns}, Renal={result.Renal}. " +
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$"Staleness: {stalenessFlags}";
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var affected = await db.Database.ExecuteSqlInterpolatedAsync($"""
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INSERT INTO clinical_alerts
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(id, encounter_id, patient_id, alert_type, severity, details, status, triggered_at)
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SELECT {alertId}, {encounterId}, {patientId},
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{alertType.ToDbString()}, {severity.ToDbString()}, {details}, 'OPEN', {triggeredAt}
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WHERE NOT EXISTS (
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SELECT 1 FROM clinical_alerts
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WHERE encounter_id = {encounterId}
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AND alert_type = {alertType.ToDbString()}
|
||||
AND status IN ('OPEN', 'ESCALATED')
|
||||
)
|
||||
""", ct);
|
||||
|
||||
if (affected == 0)
|
||||
{
|
||||
await tx.RollbackAsync(ct);
|
||||
return false;
|
||||
}
|
||||
|
||||
db.OutboxEvents.Add(new OutboxEvent
|
||||
{
|
||||
Id = Guid.NewGuid(),
|
||||
Topic = "alert.generated",
|
||||
Payload = JsonSerializer.Serialize(new
|
||||
{
|
||||
alertId,
|
||||
encounterId,
|
||||
patientId,
|
||||
alertType = alertType.ToDbString(),
|
||||
severity = severity.ToDbString(),
|
||||
details,
|
||||
triggeredAt,
|
||||
sofaTotal = result.Total,
|
||||
sofaDelta = delta,
|
||||
partitionKey = encounterId.ToString()
|
||||
}),
|
||||
PartitionKey = encounterId.ToString(),
|
||||
CreatedAt = DateTimeOffset.UtcNow
|
||||
});
|
||||
|
||||
await db.SaveChangesAsync(ct);
|
||||
await tx.CommitAsync(ct);
|
||||
|
||||
_metrics.ClinicalAlertsTotal
|
||||
.WithLabels(alertType.ToDbString(), severity.ToDbString()).Inc();
|
||||
|
||||
return true;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,65 @@
|
||||
using System.Text.Json;
|
||||
using Microsoft.Extensions.Options;
|
||||
using StackExchange.Redis;
|
||||
|
||||
public class SofaLabCache
|
||||
{
|
||||
private static readonly JsonSerializerOptions JsonOptions = new()
|
||||
{
|
||||
PropertyNameCaseInsensitive = true
|
||||
};
|
||||
|
||||
private readonly IConnectionMultiplexer _redis;
|
||||
private readonly SofaOptions _options;
|
||||
|
||||
public SofaLabCache(IConnectionMultiplexer redis, IOptions<SofaOptions> options)
|
||||
{
|
||||
_redis = redis;
|
||||
_options = options.Value;
|
||||
}
|
||||
|
||||
public async Task StoreAsync(
|
||||
Guid encounterId, string code, decimal value, DateTimeOffset recordedAt)
|
||||
{
|
||||
var json = JsonSerializer.Serialize(new SofaCachedValue(value, recordedAt), JsonOptions);
|
||||
var key = SofaCalculator.CacheKey(encounterId, code);
|
||||
await _redis.GetDatabase().StringSetAsync(
|
||||
key, json, TimeSpan.FromHours(_options.LabStalenessHours));
|
||||
}
|
||||
|
||||
public async Task<SofaCachedValue?> GetAsync(Guid encounterId, string code)
|
||||
{
|
||||
var cached = await _redis.GetDatabase()
|
||||
.StringGetAsync(SofaCalculator.CacheKey(encounterId, code));
|
||||
if (!cached.HasValue) return null;
|
||||
return JsonSerializer.Deserialize<SofaCachedValue>(cached!, JsonOptions);
|
||||
}
|
||||
|
||||
public SofaValueStatus Classify(SofaCachedValue? value)
|
||||
{
|
||||
if (value is null) return SofaValueStatus.Expired;
|
||||
var age = DateTimeOffset.UtcNow - value.RecordedAt;
|
||||
if (age.TotalHours > _options.LabStalenessHours) return SofaValueStatus.Expired;
|
||||
if (age.TotalHours > _options.LabWarningHours) return SofaValueStatus.Stale;
|
||||
return SofaValueStatus.Current;
|
||||
}
|
||||
|
||||
public async Task<Dictionary<string, SofaCachedValue>> GetAllAsync(Guid encounterId)
|
||||
{
|
||||
var cache = _redis.GetDatabase();
|
||||
var keys = SofaCalculator.SofaObservationCodes
|
||||
.Select(c => (RedisKey)SofaCalculator.CacheKey(encounterId, c))
|
||||
.ToArray();
|
||||
var values = await cache.StringGetAsync(keys);
|
||||
|
||||
var result = new Dictionary<string, SofaCachedValue>();
|
||||
for (var i = 0; i < SofaCalculator.SofaObservationCodes.Count; i++)
|
||||
{
|
||||
if (!values[i].HasValue) continue;
|
||||
var parsed = JsonSerializer.Deserialize<SofaCachedValue>(values[i]!, JsonOptions);
|
||||
if (parsed is not null)
|
||||
result[SofaCalculator.SofaObservationCodes[i]] = parsed;
|
||||
}
|
||||
return result;
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user