feature: Explainable Alerts
This commit is contained in:
voltsrage
@@ -0,0 +1,169 @@
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using System.Net.Http.Json;
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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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[Collection("Integration")]
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public class ExplainableAlertsTests : IAsyncLifetime
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{
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private readonly ApiFixture _fixture;
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public ExplainableAlertsTests(ApiFixture fixture) => _fixture = fixture;
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public async Task InitializeAsync() =>
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await ExplainableAlertsTestHelper.ResetAsync(_fixture);
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public Task DisposeAsync() => Task.CompletedTask;
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[Fact]
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public async Task News2Alert_IncludesScoreContributors()
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{
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var (encounterId, _) = await ExplainableAlertsTestHelper.SeedEncounterWithVitalsAsync(
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_fixture, respRate: 28, spo2: 92, systolicBp: 95, heartRate: 110,
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tempC: 38.5m, supplementalO2: 1m);
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var alert = await ExplainableAlertsTestHelper.WaitForAlertAsync(
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_fixture, encounterId, AlertType.News2Emergency);
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var body = await ExplainableAlertsTestHelper.GetAlertAsync<AlertResponse>(_fixture, alert.Id);
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body.Explanation.Should().NotBeNull();
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body.Explanation!.ScoreContributors.Should().HaveCount(7);
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body.Explanation.ScoreContributors.Should().Contain(c =>
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c.Parameter == "Respiratory Rate" && c.Points > 0);
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body.Explanation.NarrativeSummary.Should().NotBeNullOrWhiteSpace();
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}
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[Fact]
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public async Task SofaAlert_IncludesOrganContributors()
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{
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var (encounterId, patientId) = await ExplainableAlertsTestHelper.SeedSofaBaselineAsync(_fixture);
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await ExplainableAlertsTestHelper.AdvanceSofaDeltaAsync(_fixture, encounterId, patientId, delta: 2);
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var alert = await ExplainableAlertsTestHelper.WaitForAlertAsync(
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_fixture, encounterId, AlertType.SofaSepsis);
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var body = await ExplainableAlertsTestHelper.GetAlertAsync<AlertResponse>(_fixture, alert.Id);
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body.Explanation.Should().NotBeNull();
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body.Explanation!.ScoreContributors.Should().HaveCount(6);
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body.Explanation.ScoreContributors.Should().Contain(c => c.Parameter == "Respiratory");
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}
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[Fact]
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public async Task GcsAlert_IncludesEyeVerbalMotor()
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{
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var (encounterId, patientId) = await ExplainableAlertsTestHelper.SeedEncounterAsync(_fixture);
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await ExplainableAlertsTestHelper.RecordGcsAsync(
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_fixture, encounterId, patientId, eye: 2, verbal: 2, motor: 3);
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var alert = await ExplainableAlertsTestHelper.WaitForAlertAsync(
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_fixture, encounterId, AlertType.GcsCritical);
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var body = await ExplainableAlertsTestHelper.GetAlertAsync<AlertResponse>(_fixture, alert.Id);
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body.Explanation.Should().NotBeNull();
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body.Explanation!.ScoreContributors.Should().HaveCount(3);
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body.Explanation.ScoreContributors.Should().Contain(c => c.Parameter == "Eye");
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}
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[Fact]
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public async Task TrendAlert_IncludesTrendContext()
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{
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var (encounterId, patientId) = await ExplainableAlertsTestHelper.SeedEncounterAsync(_fixture);
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await ExplainableAlertsTestHelper.SimulateRapidRespRateRiseAsync(
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_fixture, encounterId, patientId);
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var alert = await ExplainableAlertsTestHelper.WaitForAlertAsync(
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_fixture, encounterId, AlertType.RapidDeterioration);
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var body = await ExplainableAlertsTestHelper.GetAlertAsync<AlertResponse>(_fixture, alert.Id);
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body.Explanation.Should().NotBeNull();
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body.Explanation!.Trend.Should().NotBeNull();
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body.Explanation.Trend!.PercentChange.Should().BeGreaterThan(0);
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body.Explanation.Trend.Duration.Should().NotBe(default);
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}
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[Fact]
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public async Task MedicationAlert_IncludesDrugContext()
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{
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var (encounterId, patientId) = await ExplainableAlertsTestHelper.SeedEncounterAsync(_fixture);
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await ExplainableAlertsTestHelper.AdministerMedicationAsync(
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_fixture, encounterId, "acetaminophen", dose: 1000, unit: "mg");
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await ExplainableAlertsTestHelper.FeedNews2VitalsAsync(
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_fixture, encounterId, patientId,
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respRate: 25, spo2: 91, systolicBp: 95, heartRate: 72,
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tempC: 39.2m, supplementalO2: 0m);
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var alert = await ExplainableAlertsTestHelper.WaitForFirstAlertWithExplanationAsync(
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_fixture, encounterId);
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alert.Explanation.Should().NotBeNull();
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alert.Explanation!.MedicationContext.Should().NotBeNull();
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alert.Explanation.MedicationContext!.DrugName.Should().BeEquivalentTo("acetaminophen");
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}
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[Fact]
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public async Task NarrativeSummary_IsHumanReadable()
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{
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var alert = await ExplainableAlertsTestHelper.GetAnyAlertWithExplanationAsync(_fixture);
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alert.Explanation.Should().NotBeNull();
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alert.Explanation!.NarrativeSummary.Should().MatchRegex("(NEWS2|SOFA|GCS|rapid deterioration)", "i");
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}
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[Fact]
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public async Task LegacyAlert_NullExplanation_Serializes()
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{
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var legacyId = await ExplainableAlertsTestHelper.SeedLegacyAlertWithoutExplanationAsync(_fixture);
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var body = await ExplainableAlertsTestHelper.GetAlertAsync<AlertResponse>(_fixture, legacyId);
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body.Explanation.Should().BeNull();
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}
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[Fact]
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public async Task ListByEncounter_ReturnsExplanation()
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{
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var (encounterId, _) = await ExplainableAlertsTestHelper.SeedEncounterWithVitalsAsync(
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_fixture, respRate: 25, spo2: 91, systolicBp: 95, heartRate: 72,
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tempC: 37.0m, supplementalO2: 0m);
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using var client = _fixture.CreateClient();
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var response = await client.GetAsync($"/api/v1/encounters/{encounterId}/alerts");
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response.EnsureSuccessStatusCode();
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var body = await response.Content.ReadFromJsonAsync<ApiResponse<PagedResult<AlertResponse>>>(
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ExplainableAlertsTestHelper.JsonOptions);
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body!.Data!.Items.Should().NotBeEmpty();
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body.Data.Items.Should().AllSatisfy(a =>
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{
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a.Explanation.Should().NotBeNull();
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a.Explanation!.NarrativeSummary.Should().NotBeNullOrWhiteSpace();
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});
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}
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[Fact]
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public async Task ScoringOutputs_Unchanged()
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{
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var before = await ExplainableAlertsTestHelper.RunNews2HighScoreReplayAsync(_fixture);
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var after = await ExplainableAlertsTestHelper.RunNews2HighScoreReplayAsync(_fixture);
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after.TotalScore.Should().Be(before.TotalScore);
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after.AlertType.Should().Be(before.AlertType);
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}
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[Fact]
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public async Task ExplainableAlert_OutboxPayload_IncludesExplanation()
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{
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var (encounterId, _) = await ExplainableAlertsTestHelper.SeedEncounterWithVitalsAsync(
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_fixture, respRate: 25, spo2: 91, systolicBp: 95, heartRate: 72,
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tempC: 37.0m, supplementalO2: 0m);
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using var scope = _fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var outbox = await db.OutboxEvents
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.Where(e => e.Topic == "alert.generated" && e.PartitionKey == encounterId.ToString())
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.OrderByDescending(e => e.CreatedAt)
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.FirstAsync();
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outbox.Payload.Should().Contain("explanation");
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outbox.Payload.Should().Contain("narrativeSummary");
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}
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}
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@@ -0,0 +1,299 @@
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using System.Net.Http.Json;
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using System.Text.Json;
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using System.Text.Json.Serialization;
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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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public static class ExplainableAlertsTestHelper
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{
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public static readonly JsonSerializerOptions JsonOptions = new()
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{
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PropertyNameCaseInsensitive = true,
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Converters = { new JsonStringEnumConverter() }
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};
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private static readonly DateTimeOffset TrendBaseTime =
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new(2026, 6, 18, 10, 0, 0, TimeSpan.Zero);
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public static async Task ResetAsync(ApiFixture fixture)
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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 redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
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var server = redis.GetServer(redis.GetEndPoints().First());
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await server.FlushDatabaseAsync(1);
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}
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public static async Task<(Guid EncounterId, Guid PatientId)> SeedEncounterAsync(ApiFixture fixture)
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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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var patient = new Patient
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{
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Id = Guid.NewGuid(), Mrn = $"MRN-EXP-{Guid.NewGuid():N}"[..16],
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FirstName = "Explain", LastName = "Test",
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DateOfBirth = new DateOnly(1970, 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. Explain", 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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return (encounter.Id, patient.Id);
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}
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public static async Task FeedNews2VitalsAsync(
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ApiFixture fixture, Guid encounterId, Guid patientId,
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int respRate, decimal spo2, decimal systolicBp, decimal heartRate,
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decimal tempC, decimal supplementalO2, decimal avpu = 0m)
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{
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await ClearNews2KeysAsync(fixture, encounterId);
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using var scope = fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<News2Detector>();
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await detector.ProcessObservationAsync(encounterId, patientId, "RESP_RATE", respRate);
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await detector.ProcessObservationAsync(encounterId, patientId, "SPO2", spo2);
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await detector.ProcessObservationAsync(encounterId, patientId, "SYSTOLIC_BP", systolicBp);
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await detector.ProcessObservationAsync(encounterId, patientId, "HEART_RATE", heartRate);
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await detector.ProcessObservationAsync(encounterId, patientId, "AVPU", avpu);
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await detector.ProcessObservationAsync(encounterId, patientId, "TEMP_C", tempC);
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await detector.ProcessObservationAsync(encounterId, patientId, "SUPPLEMENTAL_O2", supplementalO2);
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}
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public static async Task<(Guid EncounterId, Guid PatientId)> SeedEncounterWithVitalsAsync(
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ApiFixture fixture,
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int respRate, decimal spo2, decimal systolicBp, decimal heartRate,
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decimal tempC, decimal supplementalO2, decimal avpu = 0m)
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{
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var (encounterId, patientId) = await SeedEncounterAsync(fixture);
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await FeedNews2VitalsAsync(
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fixture, encounterId, patientId, respRate, spo2, systolicBp, heartRate,
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tempC, supplementalO2, avpu);
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return (encounterId, patientId);
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}
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public static async Task<(Guid EncounterId, Guid PatientId)> SeedSofaBaselineAsync(ApiFixture fixture)
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{
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var (encounterId, patientId) = await SeedEncounterAsync(fixture);
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await SeedSofaBaselineInputsAsync(fixture, encounterId, patientId);
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return (encounterId, patientId);
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}
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public static async Task AdvanceSofaDeltaAsync(
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ApiFixture fixture, Guid encounterId, Guid patientId, int delta = 2)
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{
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using var scope = fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<SofaDetector>();
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if (delta >= 2)
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{
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await detector.ProcessObservationAsync(encounterId, patientId, "PLATELET_K_UL", 20m, DateTimeOffset.UtcNow);
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await detector.ProcessObservationAsync(encounterId, patientId, "CREATININE_MG_DL", 4.5m, DateTimeOffset.UtcNow);
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}
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else
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{
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await detector.ProcessObservationAsync(encounterId, patientId, "PLATELET_K_UL", 120m, DateTimeOffset.UtcNow);
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}
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}
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public static async Task RecordGcsAsync(
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ApiFixture fixture, Guid encounterId, Guid patientId, int eye, int verbal, int motor)
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{
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using var scope = fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<GcsDetector>();
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await ClearGcsKeysAsync(fixture, encounterId);
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await detector.ProcessObservationAsync(encounterId, patientId, "GCS_EYE", eye);
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await detector.ProcessObservationAsync(encounterId, patientId, "GCS_VERBAL", verbal);
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await detector.ProcessObservationAsync(encounterId, patientId, "GCS_MOTOR", motor);
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}
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public static async Task SimulateRapidRespRateRiseAsync(
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ApiFixture fixture, Guid encounterId, Guid patientId)
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{
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using var scope = fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<TrendDetector>();
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await ClearTrendKeysAsync(fixture, encounterId);
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await detector.ProcessObservationAsync(
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encounterId, patientId, "RESP_RATE", 14m, TrendBaseTime);
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await detector.ProcessObservationAsync(
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encounterId, patientId, "RESP_RATE", 28m, TrendBaseTime.AddMinutes(10));
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}
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public static async Task AdministerMedicationAsync(
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ApiFixture fixture, Guid encounterId, string drugName, decimal dose, string unit)
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{
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using var scope = fixture.Services.CreateScope();
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var medService = scope.ServiceProvider.GetRequiredService<IMedicationService>();
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await medService.CreateAsync(encounterId,
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new CreateMedicationAdministrationRequest(
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drugName, dose, unit, "PO",
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DateTimeOffset.UtcNow.AddMinutes(-30), "nurse-test"));
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}
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public static async Task RecordVitalAsync(
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ApiFixture fixture, Guid encounterId, Guid patientId, string code, decimal value)
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{
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using var scope = fixture.Services.CreateScope();
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var detector = scope.ServiceProvider.GetRequiredService<News2Detector>();
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await detector.ProcessObservationAsync(encounterId, patientId, code, value);
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}
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public static async Task<ClinicalAlert> WaitForAlertAsync(
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ApiFixture fixture, Guid encounterId, AlertType alertType)
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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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var alert = await db.ClinicalAlerts
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.AsNoTracking()
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.Where(a => a.EncounterId == encounterId && a.AlertType == alertType)
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.OrderByDescending(a => a.TriggeredAt)
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.FirstOrDefaultAsync();
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if (alert is null)
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throw new InvalidOperationException(
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$"Expected {alertType} alert on encounter {encounterId} but none was found.");
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return alert;
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}
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public static async Task<T> GetAlertAsync<T>(ApiFixture fixture, Guid alertId)
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{
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using var client = fixture.CreateClient();
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var response = await client.GetAsync($"/api/v1/alerts/{alertId}");
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response.EnsureSuccessStatusCode();
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var body = await response.Content.ReadFromJsonAsync<ApiResponse<T>>(JsonOptions);
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return body!.Data!;
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}
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public static async Task<AlertResponse> WaitForFirstAlertWithExplanationAsync(
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ApiFixture fixture, Guid encounterId)
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{
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using var scope = fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var alert = await db.ClinicalAlerts
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.AsNoTracking()
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.Where(a => a.EncounterId == encounterId && a.Explanation != null)
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.OrderByDescending(a => a.TriggeredAt)
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.FirstOrDefaultAsync();
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if (alert is null)
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throw new InvalidOperationException(
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$"Expected an alert with explanation on encounter {encounterId}.");
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return await GetAlertAsync<AlertResponse>(fixture, alert.Id);
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}
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public static async Task<AlertResponse> GetAnyAlertWithExplanationAsync(ApiFixture fixture)
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{
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await SeedEncounterWithVitalsAsync(
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fixture, respRate: 25, spo2: 91, systolicBp: 95, heartRate: 72,
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tempC: 37.0m, supplementalO2: 0m);
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using var scope = fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var alert = await db.ClinicalAlerts
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.AsNoTracking()
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.Where(a => a.Explanation != null)
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.OrderByDescending(a => a.TriggeredAt)
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.FirstAsync();
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return await GetAlertAsync<AlertResponse>(fixture, alert.Id);
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}
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public static async Task<Guid> SeedLegacyAlertWithoutExplanationAsync(ApiFixture fixture)
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{
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var (encounterId, patientId) = await SeedEncounterAsync(fixture);
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using var scope = fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var alertId = Guid.NewGuid();
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db.ClinicalAlerts.Add(new ClinicalAlert
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{
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Id = alertId,
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EncounterId = encounterId,
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PatientId = patientId,
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AlertType = AlertType.CriticalPotassiumMeqL,
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Severity = AlertSeverity.Critical,
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Details = "Potassium 2.1 mEq/L is below critical low.",
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Status = AlertStatus.Open,
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TriggeredAt = DateTimeOffset.UtcNow.AddDays(-1),
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Explanation = null
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});
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await db.SaveChangesAsync();
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return alertId;
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}
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public static async Task<News2ReplayResult> RunNews2HighScoreReplayAsync(ApiFixture fixture)
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{
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var (encounterId, patientId) = await SeedEncounterWithVitalsAsync(
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fixture, respRate: 25, spo2: 91, systolicBp: 95, heartRate: 72,
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tempC: 37.0m, supplementalO2: 0m);
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using var scope = fixture.Services.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var score = await db.News2Scores
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.Where(s => s.EncounterId == encounterId)
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.OrderByDescending(s => s.CalculatedAt)
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.FirstAsync();
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var alert = await db.ClinicalAlerts
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.Where(a => a.EncounterId == encounterId)
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.OrderByDescending(a => a.TriggeredAt)
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.FirstAsync();
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return new News2ReplayResult(score.TotalScore, alert.AlertType);
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}
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private static async Task SeedSofaBaselineInputsAsync(
|
||||
ApiFixture fixture, Guid encounterId, Guid patientId)
|
||||
{
|
||||
using var scope = fixture.Services.CreateScope();
|
||||
var detector = scope.ServiceProvider.GetRequiredService<SofaDetector>();
|
||||
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "PAO2_MMHG", 100m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "FIO2_PCT", 40m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "PLATELET_K_UL", 180m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "BILIRUBIN_MG_DL", 1.0m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "SYSTOLIC_BP", 120m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "DIASTOLIC_BP", 80m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "CREATININE_MG_DL", 1.0m, DateTimeOffset.UtcNow);
|
||||
await detector.ProcessObservationAsync(encounterId, patientId, "URINE_OUTPUT_ML_H", 50m, DateTimeOffset.UtcNow);
|
||||
}
|
||||
|
||||
private static async Task ClearNews2KeysAsync(ApiFixture fixture, Guid encounterId)
|
||||
{
|
||||
using var scope = fixture.Services.CreateScope();
|
||||
var cache = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>().GetDatabase();
|
||||
foreach (var key in News2Calculator.AllParameterKeys(encounterId))
|
||||
await cache.KeyDeleteAsync(key);
|
||||
}
|
||||
|
||||
private static async Task ClearGcsKeysAsync(ApiFixture fixture, Guid encounterId)
|
||||
{
|
||||
using var scope = fixture.Services.CreateScope();
|
||||
var cache = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>().GetDatabase();
|
||||
foreach (var key in GcsCalculator.AllComponentKeys(encounterId))
|
||||
await cache.KeyDeleteAsync(key);
|
||||
}
|
||||
|
||||
private static async Task ClearTrendKeysAsync(ApiFixture fixture, Guid encounterId)
|
||||
{
|
||||
using var scope = fixture.Services.CreateScope();
|
||||
var cache = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>().GetDatabase();
|
||||
foreach (var key in TrendCalculator.AllHistoryKeys(encounterId))
|
||||
await cache.KeyDeleteAsync(key);
|
||||
}
|
||||
|
||||
public record News2ReplayResult(int TotalScore, AlertType AlertType);
|
||||
}
|
||||
Reference in New Issue
Block a user