feature: Clinical Data Model Expansion & Observation Vocabulary

2026-06-18 15:00:42 +08:00
parent 3b4c5c524b
commit 7d630fbbd9
33 changed files with 2636 additions and 36 deletions
@@ -0,0 +1,221 @@
+using System.Net;
+using System.Net.Http.Json;
+using System.Text.Json;
+using FluentAssertions;
+using Microsoft.EntityFrameworkCore;
+using Microsoft.Extensions.DependencyInjection;
+using StackExchange.Redis;
+
+[Collection("Integration")]
+public class ClinicalDemographicsAndObservationTests : IAsyncLifetime
+{
+    private readonly ApiFixture _fixture;
+    private readonly HttpClient _client;
+    private Guid _patientId;
+    private Guid _encounterId;
+
+    public ClinicalDemographicsAndObservationTests(ApiFixture fixture)
+    {
+        _fixture = fixture;
+        _client = fixture.CreateClient();
+    }
+
+    public async Task InitializeAsync()
+    {
+        using var scope = _fixture.Services.CreateScope();
+        var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
+        await DbResetHelper.ResetAsync(db);
+
+        var patient = new Patient
+        {
+            Id = Guid.NewGuid(), Mrn = "MRN-P10-001", FirstName = "Phase10", LastName = "Test",
+            DateOfBirth = new DateOnly(1965, 3, 15), Gender = "F",
+            BloodType = BloodType.BPositive, Allergies = "Sulfa",
+            EmergencyContactName = "Test Contact", EmergencyContactPhone = "555-9999",
+            CreatedAt = DateTimeOffset.UtcNow
+        };
+        var encounter = new Encounter
+        {
+            Id = Guid.NewGuid(), PatientId = patient.Id, EncounterType = EncounterType.Inpatient,
+            Status = EncounterStatus.Active, Department = Department.Icu,
+            AttendingPhysician = "Dr. Phase10",
+            RoomBed = "ICU-7A", AdmissionReason = "Sepsis workup",
+            AdmittedAt = DateTimeOffset.UtcNow, CreatedAt = DateTimeOffset.UtcNow
+        };
+        db.Patients.Add(patient);
+        db.Encounters.Add(encounter);
+
+        db.AlertThresholds.AddRange(
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "HEART_RATE",
+                DisplayName = "Heart Rate", Unit = "bpm",
+                CriticalLow = 30, WarningLow = 50, WarningHigh = 100, CriticalHigh = 150,
+                CreatedAt = DateTimeOffset.UtcNow },
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "SYSTOLIC_BP",
+                DisplayName = "Systolic BP", Unit = "mmHg",
+                CriticalLow = 70, WarningLow = 90, WarningHigh = 160, CriticalHigh = 180,
+                CreatedAt = DateTimeOffset.UtcNow },
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "DIASTOLIC_BP",
+                DisplayName = "Diastolic BP", Unit = "mmHg",
+                CriticalLow = 40, WarningLow = 60, WarningHigh = 90, CriticalHigh = 110,
+                CreatedAt = DateTimeOffset.UtcNow },
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "LACTATE_MMOL_L",
+                DisplayName = "Serum Lactate", Unit = "mmol/L",
+                CriticalLow = null, WarningLow = null, WarningHigh = 2.0m, CriticalHigh = 4.0m,
+                CreatedAt = DateTimeOffset.UtcNow },
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "AVPU",
+                DisplayName = "AVPU Consciousness", Unit = "score",
+                CriticalLow = null, WarningLow = null, WarningHigh = null, CriticalHigh = 2m,
+                CreatedAt = DateTimeOffset.UtcNow },
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "SUPPLEMENTAL_O2",
+                DisplayName = "Supplemental O2", Unit = "flag",
+                CriticalLow = null, WarningLow = null, WarningHigh = null, CriticalHigh = null,
+                CreatedAt = DateTimeOffset.UtcNow },
+            new AlertThreshold { Id = Guid.NewGuid(), ObservationCode = "GLUCOSE_MG_DL",
+                DisplayName = "Blood Glucose", Unit = "mg/dL",
+                CriticalLow = 40, WarningLow = 70, WarningHigh = 180, CriticalHigh = 400,
+                CreatedAt = DateTimeOffset.UtcNow }
+        );
+        await db.SaveChangesAsync();
+
+        var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
+        var cache = redis.GetDatabase(1);
+        foreach (var t in await db.AlertThresholds.ToListAsync())
+        {
+            var json = JsonSerializer.Serialize(new
+            {
+                t.ObservationCode, t.CriticalLow, t.WarningLow, t.WarningHigh, t.CriticalHigh
+            });
+            await cache.StringSetAsync($"threshold:{t.ObservationCode}", json);
+        }
+
+        _patientId = patient.Id;
+        _encounterId = encounter.Id;
+    }
+
+    public Task DisposeAsync() => Task.CompletedTask;
+
+    [Fact]
+    public async Task CriticalSystolicBp_AlertCreated()
+    {
+        var resp = await _client.PostAsJsonAsync(
+            $"/api/v1/encounters/{_encounterId}/observations",
+            new BatchIngestRequest(new List<IngestObservationRequest>
+            {
+                new("SYSTOLIC_BP", 65, "mmHg", ObservationSource.Device, DateTimeOffset.UtcNow, null)
+            }));
+
+        resp.StatusCode.Should().Be(HttpStatusCode.Created);
+        var body = await resp.Content.ReadFromJsonAsync<JsonDocument>();
+        body!.RootElement.GetProperty("data").GetProperty("alertGenerated").GetBoolean()
+            .Should().BeTrue();
+
+        using var scope = _fixture.Services.CreateScope();
+        var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
+        var alert = await db.ClinicalAlerts.SingleAsync();
+        alert.AlertType.Should().Be(AlertType.CriticalSystolicBp);
+        alert.Severity.Should().Be(AlertSeverity.Critical);
+    }
+
+    [Fact]
+    public async Task AvpuUnresponsive_CriticalAlert()
+    {
+        var resp = await _client.PostAsJsonAsync(
+            $"/api/v1/encounters/{_encounterId}/observations",
+            new BatchIngestRequest(new List<IngestObservationRequest>
+            {
+                new("AVPU", 3, "score", ObservationSource.Manual, DateTimeOffset.UtcNow, null)
+            }));
+
+        resp.StatusCode.Should().Be(HttpStatusCode.Created);
+
+        using var scope = _fixture.Services.CreateScope();
+        var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
+        var alert = await db.ClinicalAlerts.SingleAsync();
+        alert.AlertType.Should().Be(AlertType.CriticalAvpu);
+    }
+
+    [Fact]
+    public async Task SupplementalO2_NoAlert()
+    {
+        var resp = await _client.PostAsJsonAsync(
+            $"/api/v1/encounters/{_encounterId}/observations",
+            new BatchIngestRequest(new List<IngestObservationRequest>
+            {
+                new("SUPPLEMENTAL_O2", 1, "flag", ObservationSource.Manual, DateTimeOffset.UtcNow, null)
+            }));
+
+        resp.StatusCode.Should().Be(HttpStatusCode.Created);
+
+        using var scope = _fixture.Services.CreateScope();
+        var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
+        (await db.ClinicalAlerts.CountAsync()).Should().Be(0);
+    }
+
+    [Fact]
+    public async Task CriticalGlucose_AlertCreated()
+    {
+        var resp = await _client.PostAsJsonAsync(
+            $"/api/v1/encounters/{_encounterId}/observations",
+            new BatchIngestRequest(new List<IngestObservationRequest>
+            {
+                new("GLUCOSE_MG_DL", 30, "mg/dL", ObservationSource.Lab, DateTimeOffset.UtcNow, null)
+            }));
+
+        resp.StatusCode.Should().Be(HttpStatusCode.Created);
+
+        using var scope = _fixture.Services.CreateScope();
+        var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
+        var alert = await db.ClinicalAlerts.SingleAsync();
+        alert.AlertType.Should().Be(AlertType.CriticalGlucoseMgDl);
+    }
+
+    [Fact]
+    public async Task PatientRegistration_ClinicalFields_RoundTrip()
+    {
+        var resp = await _client.PostAsJsonAsync("/api/v1/patients", new
+        {
+            firstName = "Demo",
+            lastName = "Patient",
+            dateOfBirth = "1990-06-15",
+            gender = "M",
+            bloodType = "AB-",
+            allergies = "Latex, Iodine",
+            emergencyContactName = "Demo Contact",
+            emergencyContactPhone = "555-1234"
+        });
+
+        resp.StatusCode.Should().Be(HttpStatusCode.Created);
+        var body = await resp.Content.ReadFromJsonAsync<JsonDocument>();
+        var data = body!.RootElement.GetProperty("data");
+        data.GetProperty("bloodType").GetString().Should().Be("AB-");
+        data.GetProperty("allergies").GetString().Should().Be("Latex, Iodine");
+        data.GetProperty("emergencyContactName").GetString().Should().Be("Demo Contact");
+    }
+
+    [Fact]
+    public async Task OpenEncounter_WithRoomBed_Success()
+    {
+        var patientResp = await _client.PostAsJsonAsync("/api/v1/patients", new
+        {
+            firstName = "Room", lastName = "Test",
+            dateOfBirth = "1985-01-01", gender = "F"
+        });
+        var patientBody = await patientResp.Content.ReadFromJsonAsync<JsonDocument>();
+        var newPatientId = patientBody!.RootElement.GetProperty("data").GetProperty("id").GetGuid();
+
+        var resp = await _client.PostAsJsonAsync($"/api/v1/patients/{newPatientId}/encounters", new
+        {
+            encounterType = "INPATIENT",
+            department = "ICU",
+            attendingPhysician = "Dr. Room",
+            roomBed = "ICU-3C",
+            admissionReason = "Acute respiratory distress"
+        });
+
+        resp.StatusCode.Should().Be(HttpStatusCode.Created);
+        var body = await resp.Content.ReadFromJsonAsync<JsonDocument>();
+        var data = body!.RootElement.GetProperty("data");
+        data.GetProperty("roomBed").GetString().Should().Be("ICU-3C");
+        data.GetProperty("admissionReason").GetString().Should().Be("Acute respiratory distress");
+    }
+}
@@ -7,7 +7,8 @@ using Minio.DataModel.Args;
 using Parquet;
 using StackExchange.Redis;

-public class DataLakePhase9Tests : IClassFixture<ApiFixture>
+[Collection("Integration")]
+public class DataLakePhase9Tests
 {
    private readonly ApiFixture _fixture;
    private readonly HttpClient _http;
@@ -208,7 +209,6 @@ public class DataLakePhase9Tests : IClassFixture<ApiFixture>
        await EnsureThresholdAsync(db, "HEART_RATE", "Heart Rate", "bpm", 30, 50, 100, 150);
        await EnsureThresholdAsync(db, "POTASSIUM_MEQ_L", "Serum Potassium", "mEq/L", 2.5m, 3.5m, 5.0m, 6.5m);
        await EnsureThresholdAsync(db, "TEMP_C", "Temperature", "°C", 34m, 36m, 37.8m, 40m);
-        await db.SaveChangesAsync();

        var redis = scope.ServiceProvider.GetRequiredService<IConnectionMultiplexer>();
        var cache = redis.GetDatabase(1);
@@ -245,5 +245,15 @@ public class DataLakePhase9Tests : IClassFixture<ApiFixture>
            CriticalHigh = criticalHigh,
            CreatedAt = DateTimeOffset.UtcNow
        });
+
+        try
+        {
+            await db.SaveChangesAsync();
+        }
+        catch (DbUpdateException ex) when (
+            ex.InnerException is Npgsql.PostgresException { SqlState: "23505" })
+        {
+            // Another test inserted the same observation code concurrently.
+        }
    }
 }
@@ -4,7 +4,8 @@ using Microsoft.EntityFrameworkCore;
 using Microsoft.Extensions.DependencyInjection;
 using StackExchange.Redis;

-public class ObservabilityPhase8Tests : IClassFixture<ApiFixture>
+[Collection("Integration")]
+public class ObservabilityPhase8Tests
 {
    private static readonly string[] ExpectedMetrics =
    {