feature: qSOFA Scoring & Sepsis Bundle Compliance
This commit is contained in:
voltsrage
@@ -6,11 +6,24 @@ public static class DbResetHelper
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// the database, and preserves the schema (migrations do not re-run).
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public static async Task ResetAsync(AppDbContext db)
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{
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await db.Database.ExecuteSqlRawAsync(@"
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TRUNCATE TABLE reconciliation_alerts, outbox_events, orders,
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clinical_alerts, news2_scores, observations, encounters,
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alert_thresholds, patients
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RESTART IDENTITY CASCADE;
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");
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for (var attempt = 0; ; attempt++)
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{
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try
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{
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await db.Database.ExecuteSqlRawAsync(@"
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SET lock_timeout = '3s';
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TRUNCATE TABLE sepsis_bundle_elements, sepsis_bundles,
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reconciliation_alerts, outbox_events, orders,
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clinical_alerts, news2_scores, observations, encounters,
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alert_thresholds, patients
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RESTART IDENTITY CASCADE;
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");
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return;
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}
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catch when (attempt < 5)
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{
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await Task.Delay(1000);
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}
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}
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}
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}
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@@ -0,0 +1,37 @@
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using FluentAssertions;
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using StackExchange.Redis;
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public class QsofaCalculatorTests
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{
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[Fact]
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public void MeetsCriterion_RespRate22_ReturnsTrue() =>
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QsofaCalculator.MeetsCriterion("RESP_RATE", 22m).Should().BeTrue();
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[Fact]
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public void MeetsCriterion_RespRate21_ReturnsFalse() =>
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QsofaCalculator.MeetsCriterion("RESP_RATE", 21m).Should().BeFalse();
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[Fact]
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public void MeetsCriterion_SystolicBp100_ReturnsTrue() =>
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QsofaCalculator.MeetsCriterion("SYSTOLIC_BP", 100m).Should().BeTrue();
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[Fact]
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public void MeetsCriterion_SystolicBp101_ReturnsFalse() =>
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QsofaCalculator.MeetsCriterion("SYSTOLIC_BP", 101m).Should().BeFalse();
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[Fact]
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public void MeetsCriterion_Avpu1_ReturnsTrue() =>
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QsofaCalculator.MeetsCriterion("AVPU", 1m).Should().BeTrue();
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[Fact]
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public void MeetsCriterion_Avpu0_ReturnsFalse() =>
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QsofaCalculator.MeetsCriterion("AVPU", 0m).Should().BeFalse();
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[Fact]
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public void CountActiveCriteria_TwoOfThree_Returns2()
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{
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var values = new RedisValue[] { "24", RedisValue.Null, "95" };
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QsofaCalculator.CountActiveCriteria(values).Should().Be(2);
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}
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}
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@@ -0,0 +1,166 @@
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using FluentAssertions;
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using Microsoft.EntityFrameworkCore;
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using Microsoft.Extensions.DependencyInjection;
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using StackExchange.Redis;
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[Collection("Integration")]
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public class QsofaDetectorTests : IAsyncLifetime
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{
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private readonly ApiFixture _fixture;
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private Guid _encounterId;
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private Guid _patientId;
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public QsofaDetectorTests(ApiFixture fixture) => _fixture = fixture;
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public async Task InitializeAsync()
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{
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using var scope = _fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await DbResetHelper.ResetAsync(db);
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var patient = new Patient
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{
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Id = Guid.NewGuid(), Mrn = "MRN-QSOFA-001", FirstName = "qSOFA", LastName = "Test",
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DateOfBirth = new DateOnly(1960, 1, 1), Gender = "M",
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CreatedAt = DateTimeOffset.UtcNow
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};
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var encounter = new Encounter
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{
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Id = Guid.NewGuid(), PatientId = patient.Id, EncounterType = EncounterType.Inpatient,
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Status = EncounterStatus.Active, Department = Department.Icu,
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AttendingPhysician = "Dr. qSOFA", AdmittedAt = DateTimeOffset.UtcNow,
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CreatedAt = DateTimeOffset.UtcNow
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};
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db.Patients.Add(patient);
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db.Encounters.Add(encounter);
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await db.SaveChangesAsync();
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_patientId = patient.Id;
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_encounterId = encounter.Id;
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var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
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var cache = redis.GetDatabase();
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foreach (var key in QsofaCalculator.AllCriterionKeys(_encounterId))
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await cache.KeyDeleteAsync(key);
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}
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public Task DisposeAsync() => Task.CompletedTask;
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[Fact]
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public async Task OneCriterionMet_NoAlert()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var result = await detector.ProcessObservationAsync(
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_encounterId, _patientId, "RESP_RATE", 24m);
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result.Outcome.Should().Be(QsofaOutcome.InsufficientCriteria);
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result.ActiveCriteria.Should().Be(1);
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var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
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var ttl = await redis.GetDatabase()
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.KeyTimeToLiveAsync(QsofaCalculator.CriterionKey(_encounterId, "RESP_RATE"));
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ttl.Should().NotBeNull().And.BeGreaterThan(TimeSpan.Zero);
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}
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[Fact]
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public async Task TwoCriteriaMet_CreatesAlert()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var r1 = await detector.ProcessObservationAsync(
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_encounterId, _patientId, "RESP_RATE", 24m);
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r1.Outcome.Should().Be(QsofaOutcome.InsufficientCriteria);
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var r2 = await detector.ProcessObservationAsync(
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_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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r2.Outcome.Should().Be(QsofaOutcome.AlertCreated);
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var alert = await db.ClinicalAlerts.SingleAsync();
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alert.AlertType.Should().Be(AlertType.QsofaWarning);
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alert.Severity.Should().Be(AlertSeverity.Critical);
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alert.Status.Should().Be(AlertStatus.Open);
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alert.EncounterId.Should().Be(_encounterId);
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alert.PatientId.Should().Be(_patientId);
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alert.Details.Should().Contain("qSOFA score 2/3");
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var outbox = await db.OutboxEvents.SingleAsync();
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outbox.Topic.Should().Be("alert.generated");
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outbox.PartitionKey.Should().Be(_encounterId.ToString());
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}
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[Fact]
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public async Task CriterionNormalizes_KeyDeleted()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
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var cache = redis.GetDatabase();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var result = await detector.ProcessObservationAsync(
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_encounterId, _patientId, "RESP_RATE", 18m);
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var respKeyExists = await cache.KeyExistsAsync(
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QsofaCalculator.CriterionKey(_encounterId, "RESP_RATE"));
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respKeyExists.Should().BeFalse("a normalized respiratory rate must clear the criterion key");
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var sbpKeyExists = await cache.KeyExistsAsync(
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QsofaCalculator.CriterionKey(_encounterId, "SYSTOLIC_BP"));
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sbpKeyExists.Should().BeTrue("the other active criterion must remain in Redis");
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result.Outcome.Should().Be(QsofaOutcome.InsufficientCriteria);
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result.ActiveCriteria.Should().Be(1);
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var alert = await db.ClinicalAlerts.SingleAsync();
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alert.Status.Should().Be(AlertStatus.Open,
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"the existing alert is not auto-resolved when criteria drop below 2");
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}
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[Fact]
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public async Task DuplicateAlert_Idempotent()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var r3 = await detector.ProcessObservationAsync(
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_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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r3.Outcome.Should().Be(QsofaOutcome.AlertAlreadyOpen);
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var alertCount = await db.ClinicalAlerts.CountAsync();
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alertCount.Should().Be(1, "WHERE NOT EXISTS prevents duplicate QSOFA_WARNING while one is open");
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var outboxCount = await db.OutboxEvents.CountAsync();
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outboxCount.Should().Be(1, "outbox event must be written exactly once");
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}
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[Fact]
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public async Task NonQsofaCode_Ignored()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
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var result = await detector.ProcessObservationAsync(
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_encounterId, _patientId, "HEART_RATE", 95m);
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result.Outcome.Should().Be(QsofaOutcome.NotQsofaCode);
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foreach (var key in QsofaCalculator.AllCriterionKeys(_encounterId))
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{
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var exists = await redis.GetDatabase().KeyExistsAsync(key);
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exists.Should().BeFalse("non-qSOFA codes must not create Redis state");
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}
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}
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}
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@@ -0,0 +1,209 @@
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using FluentAssertions;
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using Microsoft.EntityFrameworkCore;
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using Microsoft.Extensions.DependencyInjection;
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using StackExchange.Redis;
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[Collection("Integration")]
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public class SepsisBundleTests : IAsyncLifetime
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{
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private readonly ApiFixture _fixture;
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private Guid _encounterId;
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private Guid _patientId;
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public SepsisBundleTests(ApiFixture fixture) => _fixture = fixture;
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public async Task InitializeAsync()
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{
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using var scope = _fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await DbResetHelper.ResetAsync(db);
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var patient = new Patient
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{
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Id = Guid.NewGuid(), Mrn = "MRN-BUNDLE-001", FirstName = "Bundle", LastName = "Test",
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DateOfBirth = new DateOnly(1965, 3, 15), Gender = "F",
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CreatedAt = DateTimeOffset.UtcNow
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};
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var encounter = new Encounter
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{
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Id = Guid.NewGuid(), PatientId = patient.Id, EncounterType = EncounterType.Inpatient,
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Status = EncounterStatus.Active, Department = Department.Icu,
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AttendingPhysician = "Dr. Bundle", AdmittedAt = DateTimeOffset.UtcNow,
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CreatedAt = DateTimeOffset.UtcNow
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};
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db.Patients.Add(patient);
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db.Encounters.Add(encounter);
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await db.SaveChangesAsync();
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_patientId = patient.Id;
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_encounterId = encounter.Id;
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var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
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var cache = redis.GetDatabase();
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foreach (var key in QsofaCalculator.AllCriterionKeys(_encounterId))
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await cache.KeyDeleteAsync(key);
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foreach (var key in SirsEvaluator.AllCriterionKeys(_encounterId))
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await cache.KeyDeleteAsync(key);
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}
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public Task DisposeAsync() => Task.CompletedTask;
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[Fact]
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public async Task QsofaAlert_CreatesBundleWithFourOrders()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var bundle = await db.SepsisBundles
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.Include(b => b.Elements)
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.SingleAsync(b => b.EncounterId == _encounterId);
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bundle.ComplianceStatus.Should().Be(SepsisBundleComplianceStatus.InProgress);
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bundle.TriggeringAlertType.Should().Be("QSOFA_WARNING");
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bundle.DeadlineAt.Should().BeCloseTo(bundle.RecognizedAt.AddHours(1), TimeSpan.FromSeconds(5));
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bundle.Elements.Should().HaveCount(4);
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var orders = await db.Orders
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.Where(o => o.EncounterId == _encounterId)
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.ToListAsync();
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orders.Should().HaveCount(4);
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orders.Should().AllSatisfy(o =>
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{
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o.Status.Should().Be(OrderStatus.Pending);
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o.Description.Should().StartWith("SEP-1:");
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o.OrderedBy.Should().Be("sepsis-bundle-engine");
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});
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var bundleOutbox = await db.OutboxEvents
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.Where(e => e.Topic == "sepsis.bundle.created")
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.SingleAsync();
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bundleOutbox.PartitionKey.Should().Be(_encounterId.ToString());
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}
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[Fact]
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public async Task SirsAlert_CreatesBundle()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<SirsDetector>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "HEART_RATE", 95m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "TEMP_C", 38.5m);
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var bundle = await db.SepsisBundles
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.Include(b => b.Elements)
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.SingleAsync(b => b.EncounterId == _encounterId);
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bundle.TriggeringAlertType.Should().Be("SEPSIS_WARNING");
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bundle.ComplianceStatus.Should().Be(SepsisBundleComplianceStatus.InProgress);
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bundle.Elements.Should().HaveCount(4);
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}
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[Fact]
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public async Task SecondAlert_IdempotentBundle()
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{
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using var scope = _fixture.Services.CreateScope();
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var qsofaDetector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var sirsDetector = scope.ServiceProvider.GetRequiredService<SirsDetector>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await qsofaDetector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await qsofaDetector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var bundleCountAfterFirst = await db.SepsisBundles.CountAsync(b => b.EncounterId == _encounterId);
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bundleCountAfterFirst.Should().Be(1);
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await sirsDetector.ProcessObservationAsync(_encounterId, _patientId, "HEART_RATE", 95m);
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await sirsDetector.ProcessObservationAsync(_encounterId, _patientId, "TEMP_C", 38.5m);
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var bundleCount = await db.SepsisBundles.CountAsync(b => b.EncounterId == _encounterId);
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bundleCount.Should().Be(1, "a second bundle must not be created while one is IN_PROGRESS");
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var orderCount = await db.Orders.CountAsync(o => o.EncounterId == _encounterId);
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orderCount.Should().Be(4, "no additional orders should be created for the duplicate bundle attempt");
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}
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[Fact]
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public async Task OrderResulted_CompletesElement()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var bundleService = scope.ServiceProvider.GetRequiredService<ISepsisBundleService>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var lactateElement = await db.SepsisBundleElements
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.Include(e => e.Order)
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.SingleAsync(e => e.ElementType == SepsisBundleElementType.SerumLactate);
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await bundleService.OnOrderResultedAsync(lactateElement.OrderId!.Value);
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var updated = await db.SepsisBundleElements
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.AsNoTracking()
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.SingleAsync(e => e.Id == lactateElement.Id);
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updated.Status.Should().Be(SepsisBundleElementStatus.Completed);
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updated.CompletedAt.Should().NotBeNull();
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var bundle = await db.SepsisBundles.AsNoTracking().SingleAsync();
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bundle.ComplianceStatus.Should().Be(SepsisBundleComplianceStatus.InProgress,
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"bundle should remain in progress until all 4 elements are completed");
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}
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[Fact]
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public async Task AllElementsResulted_BundleCompliant()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var bundleService = scope.ServiceProvider.GetRequiredService<ISepsisBundleService>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var elements = await db.SepsisBundleElements.ToListAsync();
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foreach (var element in elements)
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await bundleService.OnOrderResultedAsync(element.OrderId!.Value);
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var bundle = await db.SepsisBundles.AsNoTracking().SingleAsync();
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bundle.ComplianceStatus.Should().Be(SepsisBundleComplianceStatus.Compliant);
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bundle.CompletedAt.Should().NotBeNull();
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bundle.CompletedAt.Should().BeBefore(bundle.DeadlineAt,
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"all elements completed within the 1-hour window");
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var outboxEvents = await db.OutboxEvents
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.Where(e => e.Topic == "sepsis.bundle.updated")
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.ToListAsync();
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outboxEvents.Should().HaveCount(4, "one outbox event per element completion");
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}
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[Fact]
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public async Task DeadlinePassed_CompletionMarksNonCompliant()
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{
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using var scope = _fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<QsofaDetector>();
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var bundleService = scope.ServiceProvider.GetRequiredService<ISepsisBundleService>();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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await detector.ProcessObservationAsync(_encounterId, _patientId, "RESP_RATE", 24m);
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await detector.ProcessObservationAsync(_encounterId, _patientId, "SYSTOLIC_BP", 95m);
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var bundle = await db.SepsisBundles.SingleAsync();
|
||||
bundle.DeadlineAt = DateTimeOffset.UtcNow.AddHours(-1);
|
||||
await db.SaveChangesAsync();
|
||||
|
||||
var elements = await db.SepsisBundleElements.ToListAsync();
|
||||
foreach (var element in elements)
|
||||
await bundleService.OnOrderResultedAsync(element.OrderId!.Value);
|
||||
|
||||
var updated = await db.SepsisBundles.AsNoTracking().SingleAsync();
|
||||
updated.ComplianceStatus.Should().Be(SepsisBundleComplianceStatus.NonCompliant);
|
||||
updated.CompletedAt.Should().NotBeNull();
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user