feature: Elasticsearch CQRS Projection and Analytics Endpoints
This commit is contained in:
voltsrage
@@ -0,0 +1,94 @@
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using Elastic.Clients.Elasticsearch;
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using Elastic.Clients.Elasticsearch.IndexManagement;
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using Microsoft.Extensions.Options;
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public class ElasticIndexProvisioner : IHostedService
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{
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private readonly ElasticsearchClient _elastic;
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private readonly ElasticsearchOptions _options;
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private readonly ILogger<ElasticIndexProvisioner> _logger;
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public ElasticIndexProvisioner(
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ElasticsearchClient elastic,
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IOptions<ElasticsearchOptions> options,
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ILogger<ElasticIndexProvisioner> logger)
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{
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_elastic = elastic;
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_options = options.Value;
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_logger = logger;
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}
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public async Task StartAsync(CancellationToken cancellationToken)
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{
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await EnsureIndexAsync<PatientEncounterDocument>(
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_options.Indices.PatientEncounters, BuildPatientEncountersMapping());
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await EnsureIndexAsync<ObservationDocument>(
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_options.Indices.Observations, BuildObservationsMapping());
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await EnsureIndexAsync<ClinicalAlertDocument>(
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_options.Indices.ClinicalAlerts, BuildClinicalAlertsMapping());
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}
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private async Task EnsureIndexAsync<T>(
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string indexName,
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Action<CreateIndexRequestDescriptor<T>> configure) where T : class
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{
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var exists = await _elastic.Indices.ExistsAsync(indexName);
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if (exists.Exists)
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{
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_logger.LogInformation("Elasticsearch index '{Index}' already exists — skipping", indexName);
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return;
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}
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var resp = await _elastic.Indices.CreateAsync<T>(indexName, configure);
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if (!resp.IsValidResponse)
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throw new InvalidOperationException(
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$"Failed to create Elasticsearch index '{indexName}': {resp.DebugInformation}");
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_logger.LogInformation("Created Elasticsearch index '{Index}'", indexName);
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}
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private Action<CreateIndexRequestDescriptor<PatientEncounterDocument>> BuildPatientEncountersMapping() =>
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d => d.Mappings(m => m.Properties(p => p
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.Keyword(k => k.EncounterId)
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.Keyword(k => k.PatientId)
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.Keyword(k => k.Mrn)
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// text for full-text search + keyword sub-field for exact sort/filter
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.Text(t => t.PatientName, tf => tf
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.Fields(f => f.Keyword(k => k.PatientName)))
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.Keyword(k => k.Department)
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.Keyword(k => k.Status)
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.Keyword(k => k.AttendingPhysician)
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.Date(d => d.AdmittedAt)
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.IntegerNumber(i => i.OpenAlertCount)
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.Date(d => d.LastObservationAt!)
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));
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private Action<CreateIndexRequestDescriptor<ObservationDocument>> BuildObservationsMapping() =>
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d => d.Mappings(m => m.Properties(p => p
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.Keyword(k => k.ObservationId)
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.Keyword(k => k.EncounterId)
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.Keyword(k => k.PatientId)
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.Keyword(k => k.Mrn)
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.Keyword(k => k.ObservationCode)
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// float: observations are decimal values like 97.3, 2.5, 118.0
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// auto-mapped 'long' would truncate fractional parts silently
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.FloatNumber(f => f.Value)
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.Keyword(k => k.Unit)
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.Keyword(k => k.Source)
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.Date(d => d.RecordedAt)
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));
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private Action<CreateIndexRequestDescriptor<ClinicalAlertDocument>> BuildClinicalAlertsMapping() =>
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d => d.Mappings(m => m.Properties(p => p
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.Keyword(k => k.AlertId)
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.Keyword(k => k.EncounterId)
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.Keyword(k => k.PatientId)
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.Keyword(k => k.Department)
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.Keyword(k => k.AlertType)
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.Keyword(k => k.Severity)
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.Keyword(k => k.Status)
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.Date(d => d.TriggeredAt)
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));
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public Task StopAsync(CancellationToken cancellationToken) => Task.CompletedTask;
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}
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@@ -0,0 +1,241 @@
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using System.Text.Json;
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using Confluent.Kafka;
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using Elastic.Clients.Elasticsearch;
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using Microsoft.Extensions.Options;
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public class EsIndexerService : BackgroundService
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{
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private static readonly JsonSerializerOptions EventJsonOptions = new()
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{
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PropertyNameCaseInsensitive = true
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};
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private readonly ElasticsearchClient _elastic;
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private readonly KafkaOptions _kafkaOptions;
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private readonly ElasticsearchOptions _esOptions;
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private readonly ILogger<EsIndexerService> _logger;
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public EsIndexerService(
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ElasticsearchClient elastic,
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IOptions<KafkaOptions> kafkaOptions,
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IOptions<ElasticsearchOptions> esOptions,
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ILogger<EsIndexerService> logger)
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{
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_elastic = elastic;
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_kafkaOptions = kafkaOptions.Value;
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_esOptions = esOptions.Value;
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_logger = logger;
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}
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protected override async Task ExecuteAsync(CancellationToken stoppingToken)
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{
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var config = new ConsumerConfig
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{
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BootstrapServers = _kafkaOptions.BootstrapServers,
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GroupId = "es-indexer",
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AutoOffsetReset = AutoOffsetReset.Earliest,
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// Manual commit: offset is only committed after a successful Elasticsearch write.
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// If the process crashes between ES write and commit, the message is reprocessed.
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// Consumers must be idempotent. See idempotency contract above.
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EnableAutoCommit = false,
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EnablePartitionEof = false
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};
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using var consumer = new ConsumerBuilder<string, string>(config).Build();
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consumer.Subscribe(new[]
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{
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_kafkaOptions.Topics.ObservationRecorded,
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_kafkaOptions.Topics.AlertGenerated,
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_kafkaOptions.Topics.EncounterStatusChanged
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});
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_logger.LogInformation("EsIndexerService started. Subscribed to 3 topics.");
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try
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{
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while (!stoppingToken.IsCancellationRequested)
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{
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ConsumeResult<string, string>? result = null;
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try
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{
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result = consumer.Consume(stoppingToken);
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await DispatchAsync(result.Topic, result.Message.Value, stoppingToken);
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consumer.Commit(result);
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}
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catch (OperationCanceledException)
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{
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break;
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}
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catch (Exception ex)
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{
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_logger.LogError(ex,
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"EsIndexer failed processing topic={Topic} offset={Offset} — not committing",
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result?.Topic, result?.Offset.Value);
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// Do not commit: message will be redelivered on restart
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await Task.Delay(1000, stoppingToken);
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}
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}
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}
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finally
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{
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consumer.Close();
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}
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}
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private Task DispatchAsync(string topic, string payload, CancellationToken ct) => topic switch
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{
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var t when t == _kafkaOptions.Topics.EncounterStatusChanged =>
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HandleEncounterStatusChangedAsync(payload, ct),
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var t when t == _kafkaOptions.Topics.ObservationRecorded =>
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HandleObservationRecordedAsync(payload, ct),
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var t when t == _kafkaOptions.Topics.AlertGenerated =>
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HandleAlertGeneratedAsync(payload, ct),
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_ => Task.CompletedTask
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};
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// --- encounter.status.changed ---
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// Upserts the patient_encounters document. DocAsUpsert=true means:
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// if the document does not exist, it is created; if it exists, it is replaced.
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// Idempotent: applying the same event twice produces the same document.
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private async Task HandleEncounterStatusChangedAsync(string payload, CancellationToken ct)
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{
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var evt = JsonSerializer.Deserialize<EncounterStatusChangedEvent>(payload, EventJsonOptions)!;
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var doc = new PatientEncounterDocument
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{
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EncounterId = evt.EncounterId.ToString(),
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PatientId = evt.PatientId.ToString(),
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Mrn = evt.Mrn,
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PatientName = evt.PatientName,
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Department = evt.Department,
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Status = evt.NewStatus,
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AttendingPhysician = evt.AttendingPhysician,
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AdmittedAt = evt.AdmittedAt,
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OpenAlertCount = 0,
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LastObservationAt = null
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};
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var resp = await _elastic.UpdateAsync<PatientEncounterDocument, PatientEncounterDocument>(
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_esOptions.Indices.PatientEncounters,
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evt.EncounterId.ToString(),
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u => u.Doc(doc).DocAsUpsert(true),
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ct);
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if (!resp.IsValidResponse)
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throw new InvalidOperationException(
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$"ES upsert failed for encounter {evt.EncounterId}: {resp.DebugInformation}");
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_logger.LogDebug("Upserted patient_encounters for encounter {Id} → status={Status}",
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evt.EncounterId, evt.NewStatus);
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}
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// --- observation.recorded ---
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// Indexes the observation by observationId — idempotent PUT.
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// Also updates lastObservationAt on the parent encounter document using a script.
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private async Task HandleObservationRecordedAsync(string payload, CancellationToken ct)
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{
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var evt = JsonSerializer.Deserialize<ObservationRecordedEvent>(payload, EventJsonOptions)!;
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// Index into observations — document ID is observationId
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var doc = new ObservationDocument
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{
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ObservationId = evt.ObservationId.ToString(),
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EncounterId = evt.EncounterId.ToString(),
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PatientId = evt.PatientId.ToString(),
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Mrn = evt.Mrn ?? string.Empty,
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ObservationCode = evt.ObservationCode,
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Value = (double)evt.Value,
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Unit = evt.Unit,
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Source = evt.Source,
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RecordedAt = evt.RecordedAt
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};
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var indexResp = await _elastic.IndexAsync(
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doc,
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i => i.Index(_esOptions.Indices.Observations).Id(doc.ObservationId),
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ct);
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if (!indexResp.IsValidResponse)
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throw new InvalidOperationException(
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$"ES index failed for observation {evt.ObservationId}: {indexResp.DebugInformation}");
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// Update lastObservationAt on patient_encounters using a conditional script:
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// only update if the new recordedAt is later than the stored value.
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// This handles out-of-order delivery: an older observation re-processed after a
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// newer one must not overwrite lastObservationAt with a stale timestamp.
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var updateResp = await _elastic.UpdateAsync<PatientEncounterDocument, object>(
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_esOptions.Indices.PatientEncounters,
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evt.EncounterId.ToString(),
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u => u
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.Script(new Script(new InlineScript
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{
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Source = """
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if (ctx._source.lastObservationAt == null ||
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params.recordedAt > ctx._source.lastObservationAt) {
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ctx._source.lastObservationAt = params.recordedAt;
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}
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""",
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Language = ScriptLanguage.Painless,
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Params = new Dictionary<string, object>
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{
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["recordedAt"] = evt.RecordedAt.ToString("O")
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}
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}))
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.RetryOnConflict(3),
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ct);
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if (!updateResp.IsValidResponse && updateResp.Result != Result.NotFound)
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_logger.LogWarning(
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"Could not update lastObservationAt for encounter {Id} — encounter document may not exist yet",
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evt.EncounterId);
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}
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// --- alert.generated ---
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// Indexes the alert by alertId. Also increments openAlertCount on patient_encounters.
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// TRADE-OFF: openAlertCount increment is not idempotent for partial reprocessing.
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// It is correct for full replay from offset 0 (the stated recovery procedure).
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// For production, use a set of counted alert IDs in the script to enforce idempotency.
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private async Task HandleAlertGeneratedAsync(string payload, CancellationToken ct)
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{
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var evt = JsonSerializer.Deserialize<AlertGeneratedEvent>(payload, EventJsonOptions)!;
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var doc = new ClinicalAlertDocument
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{
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AlertId = evt.AlertId.ToString(),
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EncounterId = evt.EncounterId.ToString(),
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PatientId = evt.PatientId.ToString(),
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Department = evt.Department ?? string.Empty,
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AlertType = evt.AlertType,
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Severity = evt.Severity,
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Status = "Open",
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TriggeredAt = evt.TriggeredAt
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};
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var indexResp = await _elastic.IndexAsync(
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doc,
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i => i.Index(_esOptions.Indices.ClinicalAlerts).Id(doc.AlertId),
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ct);
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if (!indexResp.IsValidResponse)
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throw new InvalidOperationException(
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$"ES index failed for alert {evt.AlertId}: {indexResp.DebugInformation}");
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// Increment openAlertCount on the parent encounter document
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var updateResp = await _elastic.UpdateAsync<PatientEncounterDocument, object>(
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_esOptions.Indices.PatientEncounters,
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evt.EncounterId.ToString(),
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u => u
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.Script(new Script(new InlineScript
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{
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Source = "ctx._source.openAlertCount += 1",
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Language = ScriptLanguage.Painless
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}))
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.RetryOnConflict(3),
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ct);
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if (!updateResp.IsValidResponse && updateResp.Result != Result.NotFound)
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_logger.LogWarning(
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"Could not increment openAlertCount for encounter {Id}", evt.EncounterId);
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}
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}
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@@ -0,0 +1,107 @@
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using Microsoft.AspNetCore.Mvc;
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/// <summary>
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/// Elasticsearch-backed analytics queries for population, trends, alerts, and patient search.
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/// </summary>
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[ApiController]
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[Route("api/v1/analytics")]
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[Produces("application/json")]
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public class AnalyticsController : ControllerBase
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{
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private readonly IAnalyticsService _analytics;
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public AnalyticsController(IAnalyticsService analytics) => _analytics = analytics;
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/// <summary>
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/// Counts distinct patients whose observations for a code exceed or fall below a threshold in a time window.
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/// </summary>
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/// <param name="code">Observation code (e.g. HEART_RATE).</param>
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/// <param name="threshold">Numeric threshold value.</param>
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/// <param name="direction">above or below.</param>
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/// <param name="from">Optional start of recorded-at range.</param>
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/// <param name="to">Optional end of recorded-at range.</param>
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/// <returns>Cardinality of unique patients matching the criteria.</returns>
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[HttpGet("population")]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status200OK)]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status400BadRequest)]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status500InternalServerError)]
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public async Task<IActionResult> Population(
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[FromQuery] string? code,
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[FromQuery] decimal threshold,
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[FromQuery] string direction, // "above" | "below"
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[FromQuery] DateTimeOffset? from,
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[FromQuery] DateTimeOffset? to)
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{
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if (string.IsNullOrWhiteSpace(code))
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return BadRequest(ApiResponse<object>.Fail(400, "code is required.", "MISSING_CODE"));
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var result = await _analytics.GetPopulationAsync(code, threshold, direction, from, to);
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return Ok(ApiResponse<object>.Ok(result));
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}
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/// <summary>
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/// Returns hourly observation volume for an encounter and observation code.
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/// </summary>
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/// <param name="encounterId">Encounter id.</param>
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/// <param name="code">Observation code.</param>
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/// <param name="from">Optional start of recorded-at range.</param>
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/// <param name="to">Optional end of recorded-at range.</param>
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/// <returns>Hourly trend buckets with document counts.</returns>
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[HttpGet("observations/trend")]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status200OK)]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status500InternalServerError)]
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public async Task<IActionResult> ObservationTrend(
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[FromQuery] Guid encounterId,
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[FromQuery] string code,
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[FromQuery] DateTimeOffset? from,
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[FromQuery] DateTimeOffset? to)
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{
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var result = await _analytics.GetObservationTrendAsync(encounterId, code, from, to);
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return Ok(ApiResponse<object>.Ok(result));
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}
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/// <summary>
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/// Summarizes alert volume by department over a time window.
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/// </summary>
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/// <param name="severity">Optional severity filter.</param>
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/// <param name="department">Optional department filter.</param>
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/// <param name="from">Optional start of triggered-at range.</param>
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/// <param name="to">Optional end of triggered-at range.</param>
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/// <returns>Department-level counts (severity breakdown omitted in current implementation).</returns>
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[HttpGet("alerts/summary")]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status200OK)]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status500InternalServerError)]
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public async Task<IActionResult> AlertSummary(
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[FromQuery] string? severity,
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[FromQuery] string? department,
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[FromQuery] DateTimeOffset? from,
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[FromQuery] DateTimeOffset? to)
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{
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var result = await _analytics.GetAlertSummaryAsync(severity, department, from, to);
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return Ok(ApiResponse<object>.Ok(result));
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}
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/// <summary>
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/// Searches patient/encounter documents by MRN, name, department, or status.
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/// </summary>
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/// <param name="q">Free-text query (MRN, name, or department).</param>
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/// <param name="department">Optional department filter.</param>
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/// <param name="status">Optional encounter status filter.</param>
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/// <param name="page">Page number (0-based).</param>
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/// <param name="pageSize">Results per page.</param>
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/// <returns>Matching patient/encounter documents.</returns>
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[HttpGet("patients")]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status200OK)]
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[ProducesResponseType(typeof(ApiResponse<object>), StatusCodes.Status500InternalServerError)]
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public async Task<IActionResult> PatientSearch(
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[FromQuery] string? q,
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[FromQuery] string? department,
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[FromQuery] string? status,
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[FromQuery] int page = 0,
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[FromQuery] int pageSize = 20)
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{
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var result = await _analytics.SearchPatientsAsync(q, department, status, page, pageSize);
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return Ok(ApiResponse<object>.Ok(result));
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}
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}
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@@ -0,0 +1,6 @@
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public class ElasticIndexOptions
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{
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public string PatientEncounters { get; set; } = "patient_encounters";
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public string Observations { get; set; } = "observations";
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public string ClinicalAlerts { get; set; } = "clinical_alerts";
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}
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@@ -0,0 +1,6 @@
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public class ElasticsearchOptions
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{
|
||||
public const string Section = "Elasticsearch";
|
||||
public string Uri { get; set; } = null!;
|
||||
public ElasticIndexOptions Indices { get; set; } = null!;
|
||||
}
|
||||
@@ -0,0 +1,11 @@
|
||||
public class ClinicalAlertDocument
|
||||
{
|
||||
public string AlertId { get; set; } = null!;
|
||||
public string EncounterId { get; set; } = null!;
|
||||
public string PatientId { get; set; } = null!;
|
||||
public string Department { get; set; } = null!;
|
||||
public string AlertType { get; set; } = null!;
|
||||
public string Severity { get; set; } = null!;
|
||||
public string Status { get; set; } = null!;
|
||||
public DateTimeOffset TriggeredAt { get; set; }
|
||||
}
|
||||
@@ -0,0 +1,12 @@
|
||||
public class ObservationDocument
|
||||
{
|
||||
public string ObservationId { get; set; } = null!;
|
||||
public string EncounterId { get; set; } = null!;
|
||||
public string PatientId { get; set; } = null!;
|
||||
public string Mrn { get; set; } = null!;
|
||||
public string ObservationCode { get; set; } = null!;
|
||||
public double Value { get; set; }
|
||||
public string Unit { get; set; } = null!;
|
||||
public string Source { get; set; } = null!;
|
||||
public DateTimeOffset RecordedAt { get; set; }
|
||||
}
|
||||
@@ -0,0 +1,13 @@
|
||||
public class PatientEncounterDocument
|
||||
{
|
||||
public string EncounterId { get; set; } = null!;
|
||||
public string PatientId { get; set; } = null!;
|
||||
public string Mrn { get; set; } = null!;
|
||||
public string PatientName { get; set; } = null!;
|
||||
public string Department { get; set; } = null!;
|
||||
public string Status { get; set; } = null!;
|
||||
public string AttendingPhysician { get; set; } = null!;
|
||||
public DateTimeOffset AdmittedAt { get; set; }
|
||||
public int OpenAlertCount { get; set; }
|
||||
public DateTimeOffset? LastObservationAt { get; set; }
|
||||
}
|
||||
@@ -0,0 +1,3 @@
|
||||
public record AlertGeneratedEvent(
|
||||
Guid AlertId, Guid EncounterId, Guid PatientId, string? Department,
|
||||
string AlertType, string Severity, DateTimeOffset TriggeredAt);
|
||||
@@ -0,0 +1,4 @@
|
||||
public record EncounterStatusChangedEvent(
|
||||
Guid EncounterId, Guid PatientId, string Mrn, string PatientName,
|
||||
string? PreviousStatus, string NewStatus, string Department,
|
||||
string AttendingPhysician, DateTimeOffset AdmittedAt, DateTimeOffset ChangedAt);
|
||||
@@ -0,0 +1,4 @@
|
||||
public record ObservationRecordedEvent(
|
||||
Guid ObservationId, Guid EncounterId, Guid PatientId, string? Mrn,
|
||||
string ObservationCode, decimal Value, string Unit, string Source,
|
||||
DateTimeOffset RecordedAt);
|
||||
@@ -1,3 +1,4 @@
|
||||
using Elastic.Clients.Elasticsearch;
|
||||
using Microsoft.EntityFrameworkCore;
|
||||
using Serilog;
|
||||
using StackExchange.Redis;
|
||||
@@ -25,16 +26,29 @@ try
|
||||
builder.Services.Configure<KafkaOptions>(
|
||||
builder.Configuration.GetSection(KafkaOptions.Section));
|
||||
|
||||
builder.Services.Configure<ElasticsearchOptions>(
|
||||
builder.Configuration.GetSection(ElasticsearchOptions.Section));
|
||||
|
||||
var esOptions = builder.Configuration
|
||||
.GetSection(ElasticsearchOptions.Section)
|
||||
.Get<ElasticsearchOptions>()!;
|
||||
|
||||
builder.Services.AddSingleton(
|
||||
new ElasticsearchClient(new Uri(esOptions.Uri)));
|
||||
|
||||
builder.Services.AddScoped<IPatientService, PatientService>();
|
||||
builder.Services.AddScoped<IEncounterService, EncounterService>();
|
||||
builder.Services.AddScoped<IAlertThresholdService, AlertThresholdService>();
|
||||
builder.Services.AddScoped<IObservationService, ObservationService>();
|
||||
builder.Services.AddScoped<IObservationQueryService, ObservationQueryService>();
|
||||
builder.Services.AddScoped<IAlertService, AlertService>();
|
||||
builder.Services.AddScoped<IAnalyticsService, AnalyticsService>();
|
||||
|
||||
builder.Services.AddHostedService<ThresholdCacheLoader>();
|
||||
builder.Services.AddHostedService<KafkaTopicProvisioner>();
|
||||
builder.Services.AddHostedService<OutboxRelayService>();
|
||||
builder.Services.AddHostedService<ElasticIndexProvisioner>();
|
||||
builder.Services.AddHostedService<EsIndexerService>();
|
||||
|
||||
builder.Services.AddControllers()
|
||||
.AddJsonOptions(opts =>
|
||||
|
||||
@@ -0,0 +1,212 @@
|
||||
using Elastic.Clients.Elasticsearch;
|
||||
using Elastic.Clients.Elasticsearch.QueryDsl;
|
||||
using Microsoft.Extensions.Options;
|
||||
|
||||
public class AnalyticsService : IAnalyticsService
|
||||
{
|
||||
private readonly ElasticsearchClient _elastic;
|
||||
private readonly ElasticsearchOptions _options;
|
||||
|
||||
public AnalyticsService(ElasticsearchClient elastic, IOptions<ElasticsearchOptions> options)
|
||||
{
|
||||
_elastic = elastic;
|
||||
_options = options.Value;
|
||||
}
|
||||
|
||||
public async Task<object> GetPopulationAsync(string code, decimal threshold, string direction,
|
||||
DateTimeOffset? from, DateTimeOffset? to)
|
||||
{
|
||||
var filters = new List<Action<QueryDescriptor<ObservationDocument>>>
|
||||
{
|
||||
fq => fq.Term(t => t.Field(o => o.ObservationCode).Value(code))
|
||||
};
|
||||
|
||||
if (direction == "above")
|
||||
filters.Add(fq => fq.Range(r => r.NumberRange(nr =>
|
||||
nr.Field(o => o.Value).Gt((double)threshold))));
|
||||
else
|
||||
filters.Add(fq => fq.Range(r => r.NumberRange(nr =>
|
||||
nr.Field(o => o.Value).Lt((double)threshold))));
|
||||
|
||||
if (from.HasValue)
|
||||
filters.Add(fq => fq.Range(r => r.DateRange(dr =>
|
||||
dr.Field(o => o.RecordedAt).Gte(from.Value.ToString("O")))));
|
||||
|
||||
if (to.HasValue)
|
||||
filters.Add(fq => fq.Range(r => r.DateRange(dr =>
|
||||
dr.Field(o => o.RecordedAt).Lte(to.Value.ToString("O")))));
|
||||
|
||||
var resp = await _elastic.SearchAsync<ObservationDocument>(s => s
|
||||
.Indices(_options.Indices.Observations)
|
||||
.Query(q => q.Bool(b => b.Filter(filters.ToArray())))
|
||||
.Aggregations(a => a
|
||||
// cardinality: count of distinct patientId values — not a document count.
|
||||
// Two observations from the same patient count as one patient.
|
||||
.Add("unique_patients", agg => agg.Cardinality(c => c.Field(o => o.PatientId)))
|
||||
)
|
||||
.Size(0)); // no raw hits — aggregation result only
|
||||
|
||||
if (!resp.IsValidResponse)
|
||||
throw new InvalidOperationException("Elasticsearch query failed.");
|
||||
|
||||
var uniquePatients = resp.Aggregations?.GetCardinality("unique_patients")?.Value ?? 0;
|
||||
|
||||
return new
|
||||
{
|
||||
observationCode = code,
|
||||
threshold,
|
||||
direction,
|
||||
from,
|
||||
to,
|
||||
uniquePatientCount = uniquePatients
|
||||
};
|
||||
}
|
||||
|
||||
public async Task<object> GetObservationTrendAsync(Guid encounterId, string code,
|
||||
DateTimeOffset? from, DateTimeOffset? to)
|
||||
{
|
||||
var filters = new List<Action<QueryDescriptor<ObservationDocument>>>
|
||||
{
|
||||
fq => fq.Term(t => t.Field(o => o.EncounterId).Value(encounterId.ToString())),
|
||||
fq => fq.Term(t => t.Field(o => o.ObservationCode).Value(code))
|
||||
};
|
||||
|
||||
if (from.HasValue)
|
||||
filters.Add(fq => fq.Range(r => r.DateRange(dr =>
|
||||
dr.Field(o => o.RecordedAt).Gte(from.Value.ToString("O")))));
|
||||
|
||||
if (to.HasValue)
|
||||
filters.Add(fq => fq.Range(r => r.DateRange(dr =>
|
||||
dr.Field(o => o.RecordedAt).Lte(to.Value.ToString("O")))));
|
||||
|
||||
var resp = await _elastic.SearchAsync<ObservationDocument>(s => s
|
||||
.Indices(_options.Indices.Observations)
|
||||
.Query(q => q.Bool(b => b.Filter(filters.ToArray())))
|
||||
.Aggregations(a => a
|
||||
.Add("trend", agg => agg.DateHistogram(h => h
|
||||
.Field(o => o.RecordedAt)
|
||||
.CalendarInterval(Elastic.Clients.Elasticsearch.Aggregations.CalendarInterval.Hour)
|
||||
)
|
||||
)
|
||||
)
|
||||
.Size(0));
|
||||
|
||||
if (!resp.IsValidResponse)
|
||||
throw new InvalidOperationException("Elasticsearch query failed.");
|
||||
|
||||
var buckets = resp.Aggregations?.GetDateHistogram("trend")?.Buckets
|
||||
.Select(b => new
|
||||
{
|
||||
hour = b.KeyAsString,
|
||||
avg = (double?)null,
|
||||
min = (double?)null,
|
||||
max = (double?)null,
|
||||
count = b.DocCount
|
||||
}) ?? Enumerable.Empty<object>();
|
||||
|
||||
return new { encounterId, observationCode = code, trend = buckets };
|
||||
}
|
||||
|
||||
public async Task<object> GetAlertSummaryAsync(string? severity, string? department,
|
||||
DateTimeOffset? from, DateTimeOffset? to)
|
||||
{
|
||||
var filters = new List<Action<QueryDescriptor<ClinicalAlertDocument>>>();
|
||||
|
||||
if (from.HasValue)
|
||||
filters.Add(fq => fq.Range(r => r.DateRange(dr =>
|
||||
dr.Field(a => a.TriggeredAt).Gte(from.Value.ToString("O")))));
|
||||
|
||||
if (to.HasValue)
|
||||
filters.Add(fq => fq.Range(r => r.DateRange(dr =>
|
||||
dr.Field(a => a.TriggeredAt).Lte(to.Value.ToString("O")))));
|
||||
|
||||
if (!string.IsNullOrEmpty(severity))
|
||||
filters.Add(fq => fq.Term(t => t.Field(a => a.Severity).Value(severity)));
|
||||
|
||||
if (!string.IsNullOrEmpty(department))
|
||||
filters.Add(fq => fq.Term(t => t.Field(a => a.Department).Value(department)));
|
||||
|
||||
var resp = await _elastic.SearchAsync<ClinicalAlertDocument>(s => s
|
||||
.Indices(_options.Indices.ClinicalAlerts)
|
||||
.Query(q => q.Bool(b =>
|
||||
{
|
||||
if (filters.Count > 0)
|
||||
b.Filter(filters.ToArray());
|
||||
else
|
||||
b.Must(m => m.MatchAll(_ => { }));
|
||||
}))
|
||||
.Aggregations(a => a
|
||||
.Add("by_department", agg => agg.Terms(t => t
|
||||
.Field(a => a.Department).Size(50)
|
||||
)
|
||||
)
|
||||
)
|
||||
.Size(0));
|
||||
|
||||
if (!resp.IsValidResponse)
|
||||
throw new InvalidOperationException("Elasticsearch query failed.");
|
||||
|
||||
var summary = resp.Aggregations?.GetStringTerms("by_department")?.Buckets
|
||||
.Select(deptBucket => new
|
||||
{
|
||||
department = deptBucket.Key,
|
||||
total = deptBucket.DocCount,
|
||||
bySeverity = Enumerable.Empty<object>()
|
||||
}) ?? Enumerable.Empty<object>();
|
||||
|
||||
return new { from, to, summary };
|
||||
}
|
||||
|
||||
public async Task<object> SearchPatientsAsync(string? q, string? department, string? status,
|
||||
int page, int pageSize)
|
||||
{
|
||||
var filters = new List<Action<QueryDescriptor<PatientEncounterDocument>>>();
|
||||
|
||||
if (!string.IsNullOrEmpty(department))
|
||||
filters.Add(fq => fq.Term(t => t.Field(p => p.Department).Value(department)));
|
||||
|
||||
if (!string.IsNullOrEmpty(status))
|
||||
filters.Add(fq => fq.Term(t => t.Field(p => p.Status).Value(status)));
|
||||
|
||||
var resp = await _elastic.SearchAsync<PatientEncounterDocument>(s => s
|
||||
.Indices(_options.Indices.PatientEncounters)
|
||||
.Query(q2 => q2
|
||||
.Bool(b =>
|
||||
{
|
||||
if (!string.IsNullOrWhiteSpace(q))
|
||||
{
|
||||
b.Should(
|
||||
// MRN: exact keyword match — boosted because MRN lookup is
|
||||
// the most common search pattern for clinicians who know the number
|
||||
s2 => s2.Term(t => t.Field(p => p.Mrn).Value(q).Boost(3)),
|
||||
// Patient name: full-text across the analyzed field
|
||||
s2 => s2.Match(m => m.Field(p => p.PatientName).Query(q)),
|
||||
// Department: exact filter match included in should for relevance scoring
|
||||
s2 => s2.Term(t => t.Field(p => p.Department).Value(q))
|
||||
);
|
||||
b.MinimumShouldMatch(1);
|
||||
}
|
||||
else
|
||||
{
|
||||
b.Must(m => m.MatchAll(_ => { }));
|
||||
}
|
||||
|
||||
if (filters.Count > 0)
|
||||
b.Filter(filters.ToArray());
|
||||
})
|
||||
)
|
||||
.From(page * pageSize)
|
||||
.Size(pageSize));
|
||||
|
||||
if (!resp.IsValidResponse)
|
||||
throw new InvalidOperationException("Elasticsearch query failed.");
|
||||
|
||||
return new
|
||||
{
|
||||
total = resp.Total,
|
||||
page,
|
||||
pageSize,
|
||||
data = resp.Documents
|
||||
};
|
||||
}
|
||||
}
|
||||
@@ -34,7 +34,10 @@ public class EncounterService : IEncounterService
|
||||
public async Task<EncounterStatusTransitionResult> TransitionStatusAsync(
|
||||
Guid encounterId, EncounterStatus targetStatus)
|
||||
{
|
||||
var encounter = await _db.Encounters.FindAsync(encounterId);
|
||||
var encounter = await _db.Encounters
|
||||
.Include(e => e.Patient)
|
||||
.FirstOrDefaultAsync(e => e.Id == encounterId);
|
||||
|
||||
if (encounter is null)
|
||||
throw new NotFoundException("Encounter not found.", "ENCOUNTER_NOT_FOUND");
|
||||
|
||||
@@ -57,8 +60,13 @@ public class EncounterService : IEncounterService
|
||||
{
|
||||
encounterId,
|
||||
patientId = encounter.PatientId,
|
||||
mrn = encounter.Patient.Mrn,
|
||||
patientName = $"{encounter.Patient.FirstName} {encounter.Patient.LastName}",
|
||||
previousStatus = previousStatus.ToDbString(),
|
||||
newStatus = targetStatus.ToDbString(),
|
||||
department = encounter.Department,
|
||||
attendingPhysician = encounter.AttendingPhysician,
|
||||
admittedAt = encounter.AdmittedAt,
|
||||
changedAt = DateTimeOffset.UtcNow
|
||||
}),
|
||||
PartitionKey = encounterId.ToString(),
|
||||
|
||||
@@ -0,0 +1,11 @@
|
||||
public interface IAnalyticsService
|
||||
{
|
||||
Task<object> GetPopulationAsync(string code, decimal threshold, string direction,
|
||||
DateTimeOffset? from, DateTimeOffset? to);
|
||||
Task<object> GetObservationTrendAsync(Guid encounterId, string code,
|
||||
DateTimeOffset? from, DateTimeOffset? to);
|
||||
Task<object> GetAlertSummaryAsync(string? severity, string? department,
|
||||
DateTimeOffset? from, DateTimeOffset? to);
|
||||
Task<object> SearchPatientsAsync(string? q, string? department, string? status,
|
||||
int page, int pageSize);
|
||||
}
|
||||
@@ -22,6 +22,7 @@ public class ObservationService : IObservationService
|
||||
{
|
||||
// Step 1 — encounter must be active
|
||||
var encounter = await _db.Encounters
|
||||
.Include(e => e.Patient)
|
||||
.AsNoTracking()
|
||||
.FirstOrDefaultAsync(e => e.Id == encounterId);
|
||||
|
||||
@@ -112,6 +113,7 @@ public class ObservationService : IObservationService
|
||||
alertId = alert.Id,
|
||||
encounterId,
|
||||
patientId = encounter.PatientId,
|
||||
department = encounter.Department,
|
||||
alertType = alert.AlertType.ToDbString(),
|
||||
severity = alert.Severity.ToDbString(),
|
||||
triggeredAt = alert.TriggeredAt,
|
||||
@@ -125,6 +127,7 @@ public class ObservationService : IObservationService
|
||||
observationId = observation.Id,
|
||||
encounterId,
|
||||
patientId = encounter.PatientId,
|
||||
mrn = encounter.Patient?.Mrn,
|
||||
observationCode = req.ObservationCode,
|
||||
value = req.Value,
|
||||
unit = req.Unit,
|
||||
|
||||
@@ -1,3 +1,4 @@
|
||||
using System.Text.Json;
|
||||
using Microsoft.EntityFrameworkCore;
|
||||
|
||||
public class PatientService : IPatientService
|
||||
@@ -87,6 +88,28 @@ public class PatientService : IPatientService
|
||||
CreatedAt = DateTimeOffset.UtcNow
|
||||
};
|
||||
_db.Encounters.Add(encounter);
|
||||
|
||||
_db.OutboxEvents.Add(new OutboxEvent
|
||||
{
|
||||
Id = Guid.NewGuid(),
|
||||
Topic = "encounter.status.changed",
|
||||
Payload = JsonSerializer.Serialize(new
|
||||
{
|
||||
encounterId = encounter.Id,
|
||||
patientId = patient.Id,
|
||||
mrn = patient.Mrn,
|
||||
patientName = $"{patient.FirstName} {patient.LastName}",
|
||||
previousStatus = (string?)null,
|
||||
newStatus = encounter.Status.ToDbString(),
|
||||
department = encounter.Department,
|
||||
attendingPhysician = encounter.AttendingPhysician,
|
||||
admittedAt = encounter.AdmittedAt,
|
||||
changedAt = DateTimeOffset.UtcNow
|
||||
}),
|
||||
PartitionKey = encounter.Id.ToString(),
|
||||
CreatedAt = DateTimeOffset.UtcNow
|
||||
});
|
||||
|
||||
await _db.SaveChangesAsync();
|
||||
return encounter;
|
||||
}
|
||||
|
||||
@@ -10,6 +10,7 @@
|
||||
|
||||
<ItemGroup>
|
||||
<PackageReference Include="Confluent.Kafka" Version="2.14.0" />
|
||||
<PackageReference Include="Elastic.Clients.Elasticsearch" Version="8.13.12" />
|
||||
<PackageReference Include="Microsoft.AspNetCore.OpenApi" Version="8.0.27" />
|
||||
<PackageReference Include="Microsoft.EntityFrameworkCore.Tools" Version="8.0.4">
|
||||
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
|
||||
|
||||
@@ -46,5 +46,13 @@
|
||||
"NumPartitions": 6,
|
||||
"OutboxBatchSize": 100,
|
||||
"OutboxPollIntervalMs": 500
|
||||
},
|
||||
"Elasticsearch": {
|
||||
"Uri": "http://localhost:9200",
|
||||
"Indices": {
|
||||
"PatientEncounters": "patient_encounters",
|
||||
"Observations": "observations",
|
||||
"ClinicalAlerts": "clinical_alerts"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
+21
-1
@@ -50,7 +50,27 @@ services:
|
||||
volumes:
|
||||
- kafka_data:/var/lib/kafka/data
|
||||
|
||||
elasticsearch:
|
||||
image: docker.elastic.co/elasticsearch/elasticsearch:8.13.0
|
||||
environment:
|
||||
- discovery.type=single-node
|
||||
# Security disabled for development — no TLS negotiation overhead, no keystore setup.
|
||||
# A production deployment would enable xpack.security and use HTTPS.
|
||||
- xpack.security.enabled=false
|
||||
- ES_JAVA_OPTS=-Xms512m -Xmx512m
|
||||
- cluster.name=vigilcare-dev
|
||||
ports:
|
||||
- "9200:9200"
|
||||
volumes:
|
||||
- es_data:/usr/share/elasticsearch/data
|
||||
healthcheck:
|
||||
test: ["CMD", "curl", "-f", "http://localhost:9200/_cluster/health"]
|
||||
interval: 10s
|
||||
timeout: 5s
|
||||
retries: 10
|
||||
|
||||
volumes:
|
||||
pg_data:
|
||||
seq_data:
|
||||
kafka_data:
|
||||
kafka_data:
|
||||
es_data:
|
||||
Executable
+478
@@ -0,0 +1,478 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
set -euo pipefail
|
||||
|
||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||
COMPOSE_FILE="${COMPOSE_FILE:-${SCRIPT_DIR}/../docker-compose.yml}"
|
||||
|
||||
BASE_URL="${BASE_URL:-http://localhost:5270}"
|
||||
ES_URL="${ES_URL:-http://localhost:9200}"
|
||||
PGHOST="${PGHOST:-localhost}"
|
||||
PGPORT="${PGPORT:-5436}"
|
||||
PGDATABASE="${PGDATABASE:-vigilcare}"
|
||||
PGUSER="${PGUSER:-postgres}"
|
||||
PGPASSWORD="${PGPASSWORD:-password}"
|
||||
|
||||
ES_CONSUMER_GROUP="${ES_CONSUMER_GROUP:-es-indexer}"
|
||||
INDEX_WAIT_SECS="${INDEX_WAIT_SECS:-60}"
|
||||
RELAY_WAIT_SECS="${RELAY_WAIT_SECS:-45}"
|
||||
KAFKA_READY_WAIT_SECS="${KAFKA_READY_WAIT_SECS:-30}"
|
||||
|
||||
SCRIPT_RUN_ID="$(date -u +"%Y%m%d%H%M%S")"
|
||||
|
||||
# Per-run time windows so analytics assertions are isolated from prior script runs.
|
||||
_pop_month="$(echo "$SCRIPT_RUN_ID" | cut -c5-6)"
|
||||
_pop_day="$(echo "$SCRIPT_RUN_ID" | cut -c7-8)"
|
||||
_pop_hour="$(echo "$SCRIPT_RUN_ID" | cut -c9-10)"
|
||||
_pop_min="$(echo "$SCRIPT_RUN_ID" | cut -c11-12)"
|
||||
_pop_sec="$(echo "$SCRIPT_RUN_ID" | cut -c13-14)"
|
||||
POPULATION_AT="2099-${_pop_month}-${_pop_day}T${_pop_hour}:${_pop_min}:${_pop_sec}Z"
|
||||
POPULATION_FROM="${POPULATION_AT}"
|
||||
POPULATION_TO="${POPULATION_AT}"
|
||||
TREND_DAY="2099-${_pop_month}-${_pop_day}"
|
||||
TREND_FROM="${TREND_DAY}T00:00:00Z"
|
||||
TREND_TO="${TREND_DAY}T12:00:00Z"
|
||||
TREND_AT_HOUR_1="${TREND_DAY}T01:30:00Z"
|
||||
TREND_AT_HOUR_3="${TREND_DAY}T03:45:00Z"
|
||||
ALERT_AT="2099-${_pop_month}-${_pop_day}T${_pop_hour}:${_pop_min}:${_pop_sec}Z"
|
||||
|
||||
TMP_FILES=()
|
||||
|
||||
cleanup() {
|
||||
local f
|
||||
for f in "${TMP_FILES[@]}"; do
|
||||
rm -f "${f}" "${f}.status" 2>/dev/null || true
|
||||
done
|
||||
}
|
||||
trap cleanup EXIT
|
||||
|
||||
if ! command -v curl >/dev/null 2>&1; then
|
||||
echo "Missing dependency: curl"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if ! command -v jq >/dev/null 2>&1; then
|
||||
echo "Missing dependency: jq"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if ! command -v docker >/dev/null 2>&1 || [[ ! -f "${COMPOSE_FILE}" ]]; then
|
||||
echo "Missing dependency: docker compose (${COMPOSE_FILE})"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
compose() {
|
||||
docker compose -f "${COMPOSE_FILE}" "$@"
|
||||
}
|
||||
|
||||
kafka_exec() {
|
||||
compose exec -T kafka "$@"
|
||||
}
|
||||
|
||||
psql_cmd() {
|
||||
local sql="$1"
|
||||
if command -v psql >/dev/null 2>&1; then
|
||||
PGPASSWORD="${PGPASSWORD}" psql -h "${PGHOST}" -p "${PGPORT}" -U "${PGUSER}" -d "${PGDATABASE}" -tAc "${sql}"
|
||||
else
|
||||
compose exec -T postgres psql -U "${PGUSER}" -d "${PGDATABASE}" -tAc "${sql}"
|
||||
fi
|
||||
}
|
||||
|
||||
request() {
|
||||
local method="$1"
|
||||
local url="$2"
|
||||
local body="${3:-}"
|
||||
local tmp_body
|
||||
tmp_body="$(mktemp)"
|
||||
TMP_FILES+=("${tmp_body}")
|
||||
local status
|
||||
|
||||
if [[ -n "${body}" ]]; then
|
||||
status="$(curl -sS -o "${tmp_body}" -w "%{http_code}" -X "${method}" "${url}" \
|
||||
-H "Content-Type: application/json" -d "${body}")"
|
||||
else
|
||||
status="$(curl -sS -o "${tmp_body}" -w "%{http_code}" -X "${method}" "${url}")"
|
||||
fi
|
||||
|
||||
echo "${status}" > "${tmp_body}.status"
|
||||
echo "${tmp_body}"
|
||||
}
|
||||
|
||||
assert_status() {
|
||||
local expected="$1"
|
||||
local body_file="$2"
|
||||
local status
|
||||
status="$(cat "${body_file}.status")"
|
||||
if [[ "${status}" != "${expected}" ]]; then
|
||||
echo "Expected HTTP ${expected}, got ${status}"
|
||||
echo "Response body:"
|
||||
cat "${body_file}"
|
||||
echo
|
||||
return 1
|
||||
fi
|
||||
}
|
||||
|
||||
es_count() {
|
||||
local index="$1"
|
||||
curl -sS "${ES_URL}/${index}/_count" | jq -r '.count'
|
||||
}
|
||||
|
||||
es_encounter_source() {
|
||||
local encounter_id="$1"
|
||||
curl -sS "${ES_URL}/patient_encounters/_source/${encounter_id}"
|
||||
}
|
||||
|
||||
wait_for_kafka() {
|
||||
local elapsed=0
|
||||
while (( elapsed < KAFKA_READY_WAIT_SECS )); do
|
||||
if kafka_exec /opt/kafka/bin/kafka-broker-api-versions.sh --bootstrap-server localhost:9092 >/dev/null 2>&1; then
|
||||
return 0
|
||||
fi
|
||||
sleep 2
|
||||
elapsed=$((elapsed + 2))
|
||||
done
|
||||
echo "Kafka did not become ready within ${KAFKA_READY_WAIT_SECS}s"
|
||||
return 1
|
||||
}
|
||||
|
||||
indexer_lag() {
|
||||
kafka_exec /opt/kafka/bin/kafka-consumer-groups.sh \
|
||||
--bootstrap-server localhost:9092 \
|
||||
--describe \
|
||||
--group "${ES_CONSUMER_GROUP}" 2>/dev/null | \
|
||||
awk 'NR > 1 && $1 != "" { sum += $6 } END { print sum + 0 }'
|
||||
}
|
||||
|
||||
wait_for_indexer_lag_zero() {
|
||||
local elapsed=0
|
||||
while (( elapsed < INDEX_WAIT_SECS )); do
|
||||
local lag
|
||||
lag="$(indexer_lag)"
|
||||
if [[ "${lag}" == "0" ]]; then
|
||||
return 0
|
||||
fi
|
||||
sleep 2
|
||||
elapsed=$((elapsed + 2))
|
||||
done
|
||||
echo "es-indexer lag did not reach zero within ${INDEX_WAIT_SECS}s (lag=${lag:-unknown})"
|
||||
return 1
|
||||
}
|
||||
|
||||
wait_for_outbox_processed() {
|
||||
local outbox_id="$1"
|
||||
local elapsed=0
|
||||
while (( elapsed < RELAY_WAIT_SECS )); do
|
||||
local processed
|
||||
processed="$(psql_cmd "SELECT processed_at IS NOT NULL FROM outbox_events WHERE id = '${outbox_id}'")"
|
||||
if [[ "${processed}" == "t" ]]; then
|
||||
return 0
|
||||
fi
|
||||
sleep 1
|
||||
elapsed=$((elapsed + 1))
|
||||
done
|
||||
echo "Outbox row ${outbox_id} was not processed within ${RELAY_WAIT_SECS}s"
|
||||
return 1
|
||||
}
|
||||
|
||||
assert_projection_counts_match() {
|
||||
local relayed_obs relayed_enc relayed_alerts es_obs es_enc es_alerts
|
||||
relayed_obs="$(psql_cmd "SELECT COUNT(*) FROM outbox_events WHERE topic = 'observation.recorded' AND processed_at IS NOT NULL")"
|
||||
relayed_enc="$(psql_cmd "SELECT COUNT(*) FROM outbox_events WHERE topic = 'encounter.status.changed' AND processed_at IS NOT NULL")"
|
||||
relayed_alerts="$(psql_cmd "SELECT COUNT(*) FROM outbox_events WHERE topic = 'alert.generated' AND processed_at IS NOT NULL")"
|
||||
es_obs="$(es_count observations)"
|
||||
es_enc="$(es_count patient_encounters)"
|
||||
es_alerts="$(es_count clinical_alerts)"
|
||||
|
||||
if [[ "${relayed_obs}" != "${es_obs}" ]]; then
|
||||
echo "Observation projection mismatch: relayed=${relayed_obs}, Elasticsearch=${es_obs}"
|
||||
return 1
|
||||
fi
|
||||
if [[ "${relayed_enc}" != "${es_enc}" ]]; then
|
||||
echo "Encounter projection mismatch: relayed=${relayed_enc}, Elasticsearch=${es_enc}"
|
||||
return 1
|
||||
fi
|
||||
if [[ "${relayed_alerts}" != "${es_alerts}" ]]; then
|
||||
echo "Clinical alert projection mismatch: relayed=${relayed_alerts}, Elasticsearch=${es_alerts}"
|
||||
return 1
|
||||
fi
|
||||
echo "OK: Elasticsearch counts match relayed outbox events (obs=${es_obs}, enc=${es_enc}, alerts=${es_alerts})"
|
||||
}
|
||||
|
||||
ingest_observation() {
|
||||
local encounter_id="$1"
|
||||
local code="$2"
|
||||
local value="$3"
|
||||
local unit="$4"
|
||||
local source="$5"
|
||||
local recorded_at="$6"
|
||||
local idempotency_key="$7"
|
||||
|
||||
local payload
|
||||
payload="$(jq -nc \
|
||||
--arg code "${code}" \
|
||||
--argjson value "${value}" \
|
||||
--arg unit "${unit}" \
|
||||
--arg source "${source}" \
|
||||
--arg recordedAt "${recorded_at}" \
|
||||
--arg key "${idempotency_key}" \
|
||||
'{observations:[{observationCode:$code,value:$value,unit:$unit,source:$source,recordedAt:$recordedAt,idempotencyKey:$key}]}')"
|
||||
|
||||
local resp
|
||||
resp="$(request POST "${BASE_URL}/api/v1/encounters/${encounter_id}/observations" "${payload}")"
|
||||
assert_status "201" "${resp}"
|
||||
}
|
||||
|
||||
TOTAL_STEPS=17
|
||||
|
||||
echo "Running Elasticsearch + analytics verification against ${BASE_URL}"
|
||||
echo "Script run id: ${SCRIPT_RUN_ID}"
|
||||
|
||||
echo ""
|
||||
echo "[0/${TOTAL_STEPS}] Preflight — API, Postgres, Kafka, and Elasticsearch reachable"
|
||||
preflight_status="$(curl -sS -o /dev/null -w "%{http_code}" "${BASE_URL}/api/v1/alert-thresholds" || true)"
|
||||
if [[ "${preflight_status}" != "200" ]]; then
|
||||
echo "API not reachable at ${BASE_URL} (HTTP ${preflight_status})."
|
||||
echo "Start the API with: dotnet run --project VigilCareClinicalAPI"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if ! psql_cmd "SELECT 1" >/dev/null 2>&1; then
|
||||
echo "Postgres not reachable on ${PGHOST}:${PGPORT}."
|
||||
echo "Start the stack with: docker compose up -d"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if ! wait_for_kafka; then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
es_health_status="$(curl -sS "${ES_URL}/_cluster/health" | jq -r '.status' || true)"
|
||||
if [[ "${es_health_status}" != "green" && "${es_health_status}" != "yellow" ]]; then
|
||||
echo "Elasticsearch cluster health is '${es_health_status}' (expected green or yellow)."
|
||||
echo "Start the stack with: docker compose up -d"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: API, Postgres, Kafka, and Elasticsearch are up (cluster=${es_health_status})"
|
||||
|
||||
echo ""
|
||||
echo "[1/${TOTAL_STEPS}] Verifying Elasticsearch indices exist"
|
||||
for index in patient_encounters observations clinical_alerts; do
|
||||
exists="$(curl -sS -o /dev/null -w "%{http_code}" "${ES_URL}/${index}" || true)"
|
||||
if [[ "${exists}" != "200" ]]; then
|
||||
echo "Missing Elasticsearch index: ${index} (HTTP ${exists})"
|
||||
exit 1
|
||||
fi
|
||||
done
|
||||
echo "OK: patient_encounters, observations, clinical_alerts indices exist"
|
||||
|
||||
echo ""
|
||||
echo "[2/${TOTAL_STEPS}] Waiting for es-indexer consumer lag to reach zero"
|
||||
if ! wait_for_indexer_lag_zero; then
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: es-indexer lag is zero"
|
||||
|
||||
echo ""
|
||||
echo "[3/${TOTAL_STEPS}] Verifying Elasticsearch document counts match relayed outbox events"
|
||||
assert_projection_counts_match
|
||||
|
||||
echo ""
|
||||
echo "[4/${TOTAL_STEPS}] Creating patient and two ICU encounters for analytics fixtures"
|
||||
patient_payload='{"firstName":"Verify","lastName":"Smith","dateOfBirth":"1985-03-20","gender":"F"}'
|
||||
resp="$(request POST "${BASE_URL}/api/v1/patients" "${patient_payload}")"
|
||||
assert_status "201" "${resp}"
|
||||
patient_id="$(jq -r '.data.id' "${resp}")"
|
||||
patient_mrn="$(jq -r '.data.mrn' "${resp}")"
|
||||
if [[ -z "${patient_mrn}" || "${patient_mrn}" == "null" ]]; then
|
||||
echo "Could not parse patient MRN from create response."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
enc_payload_a='{"encounterType":"Inpatient","department":"ICU","attendingPhysician":"Dr. Elastic"}'
|
||||
resp="$(request POST "${BASE_URL}/api/v1/patients/${patient_id}/encounters" "${enc_payload_a}")"
|
||||
assert_status "201" "${resp}"
|
||||
encounter_a="$(jq -r '.data.id' "${resp}")"
|
||||
|
||||
enc_payload_b='{"encounterType":"Outpatient","department":"ICU","attendingPhysician":"Dr. Elastic"}'
|
||||
resp="$(request POST "${BASE_URL}/api/v1/patients/${patient_id}/encounters" "${enc_payload_b}")"
|
||||
assert_status "201" "${resp}"
|
||||
encounter_b="$(jq -r '.data.id' "${resp}")"
|
||||
echo "OK: patient ${patient_id} (mrn=${patient_mrn}), encounters ${encounter_a}, ${encounter_b}"
|
||||
|
||||
echo ""
|
||||
echo "[5/${TOTAL_STEPS}] Waiting for encounter documents to appear in Elasticsearch"
|
||||
elapsed=0
|
||||
while (( elapsed < INDEX_WAIT_SECS )); do
|
||||
source="$(es_encounter_source "${encounter_a}" 2>/dev/null || true)"
|
||||
if jq -e '.encounterId' >/dev/null 2>&1 <<< "${source}"; then
|
||||
break
|
||||
fi
|
||||
sleep 2
|
||||
elapsed=$((elapsed + 2))
|
||||
done
|
||||
if ! jq -e '.encounterId' >/dev/null 2>&1 <<< "$(es_encounter_source "${encounter_a}")"; then
|
||||
echo "patient_encounters document not found for encounter ${encounter_a}"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: patient_encounters documents indexed"
|
||||
|
||||
echo ""
|
||||
echo "[6/${TOTAL_STEPS}] Verifying openAlertCount is zero before any alert"
|
||||
open_before="$(es_encounter_source "${encounter_a}" | jq -r '.openAlertCount')"
|
||||
if [[ "${open_before}" != "0" ]]; then
|
||||
echo "Expected openAlertCount=0 before alert, got ${open_before}"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: openAlertCount=0 before critical ingest"
|
||||
|
||||
echo ""
|
||||
echo "[7/${TOTAL_STEPS}] Ingesting population, trend, and critical observations"
|
||||
ingest_observation "${encounter_a}" "HEART_RATE" 104 "bpm" "DEVICE" "${POPULATION_AT}" \
|
||||
"es-pop-a1-${SCRIPT_RUN_ID}"
|
||||
ingest_observation "${encounter_a}" "HEART_RATE" 112 "bpm" "DEVICE" "${POPULATION_AT}" \
|
||||
"es-pop-a2-${SCRIPT_RUN_ID}"
|
||||
ingest_observation "${encounter_b}" "HEART_RATE" 82 "bpm" "DEVICE" "${POPULATION_AT}" \
|
||||
"es-pop-b1-${SCRIPT_RUN_ID}"
|
||||
ingest_observation "${encounter_a}" "HEART_RATE" 90 "bpm" "DEVICE" "${TREND_AT_HOUR_1}" \
|
||||
"es-trend-h1-${SCRIPT_RUN_ID}"
|
||||
ingest_observation "${encounter_a}" "HEART_RATE" 95 "bpm" "DEVICE" "${TREND_AT_HOUR_3}" \
|
||||
"es-trend-h3-${SCRIPT_RUN_ID}"
|
||||
|
||||
critical_payload="$(jq -nc \
|
||||
--arg recordedAt "${ALERT_AT}" \
|
||||
--arg key "es-critical-${SCRIPT_RUN_ID}" \
|
||||
'{observations:[{observationCode:"POTASSIUM_MEQ_L",value:2.1,unit:"mEq/L",source:"LAB",recordedAt:$recordedAt,idempotencyKey:$key}]}')"
|
||||
resp="$(request POST "${BASE_URL}/api/v1/encounters/${encounter_a}/observations" "${critical_payload}")"
|
||||
assert_status "201" "${resp}"
|
||||
if [[ "$(jq -r '.data.alertGenerated' "${resp}")" != "true" ]]; then
|
||||
echo "Expected critical potassium ingest to generate an alert"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: five observations and one critical alert ingested"
|
||||
|
||||
echo ""
|
||||
echo "[8/${TOTAL_STEPS}] Waiting for outbox relay and es-indexer to catch up"
|
||||
latest_outbox="$(psql_cmd "SELECT id FROM outbox_events ORDER BY created_at DESC LIMIT 1")"
|
||||
if [[ -n "${latest_outbox}" ]]; then
|
||||
wait_for_outbox_processed "${latest_outbox}"
|
||||
fi
|
||||
if ! wait_for_indexer_lag_zero; then
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: relay and es-indexer caught up"
|
||||
|
||||
echo ""
|
||||
echo "[9/${TOTAL_STEPS}] Re-verifying projection counts after ingest"
|
||||
assert_projection_counts_match
|
||||
|
||||
echo ""
|
||||
echo "[10/${TOTAL_STEPS}] Verifying population query cardinality (uniquePatientCount = 1)"
|
||||
population_url="${BASE_URL}/api/v1/analytics/population?code=HEART_RATE&threshold=100&direction=above&from=${POPULATION_FROM}&to=${POPULATION_TO}"
|
||||
resp="$(request GET "${population_url}")"
|
||||
assert_status "200" "${resp}"
|
||||
if ! jq -e '.data.uniquePatientCount == 1' "${resp}" >/dev/null; then
|
||||
echo "Expected uniquePatientCount=1 for two above-threshold observations from one patient"
|
||||
echo "Response body:"
|
||||
cat "${resp}"
|
||||
echo
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: population query returned uniquePatientCount=1"
|
||||
|
||||
echo ""
|
||||
echo "[11/${TOTAL_STEPS}] Verifying observation trend hourly buckets"
|
||||
trend_url="${BASE_URL}/api/v1/analytics/observations/trend?encounterId=${encounter_a}&code=HEART_RATE&from=${TREND_FROM}&to=${TREND_TO}"
|
||||
resp="$(request GET "${trend_url}")"
|
||||
assert_status "200" "${resp}"
|
||||
trend_count="$(jq -r '.data.trend | length' "${resp}")"
|
||||
if [[ "${trend_count}" -lt 2 ]]; then
|
||||
echo "Expected at least two hourly trend buckets, got ${trend_count}"
|
||||
echo "Response body:"
|
||||
cat "${resp}"
|
||||
echo
|
||||
exit 1
|
||||
fi
|
||||
if ! jq -e '.data.trend[] | select(.count >= 1)' "${resp}" >/dev/null; then
|
||||
echo "Expected trend buckets with count >= 1"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: trend query returned ${trend_count} hourly bucket(s)"
|
||||
|
||||
echo ""
|
||||
echo "[12/${TOTAL_STEPS}] Verifying patient search by exact MRN"
|
||||
search_url="${BASE_URL}/api/v1/analytics/patients?q=${patient_mrn}"
|
||||
resp="$(request GET "${search_url}")"
|
||||
assert_status "200" "${resp}"
|
||||
if ! jq -e --arg mrn "${patient_mrn}" '.data.data[] | select(.mrn == $mrn)' "${resp}" >/dev/null; then
|
||||
echo "MRN search did not return patient with mrn=${patient_mrn}"
|
||||
echo "Response body:"
|
||||
cat "${resp}"
|
||||
echo
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: MRN search returned exact match (${patient_mrn})"
|
||||
|
||||
echo ""
|
||||
echo "[13/${TOTAL_STEPS}] Verifying patient search by partial name"
|
||||
resp="$(request GET "${BASE_URL}/api/v1/analytics/patients?q=smith")"
|
||||
assert_status "200" "${resp}"
|
||||
if ! jq -e --arg id "${patient_id}" '.data.data[] | select(.patientId == $id)' "${resp}" >/dev/null; then
|
||||
echo "Name search for 'smith' did not return patient ${patient_id}"
|
||||
echo "Response body:"
|
||||
cat "${resp}"
|
||||
echo
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: partial name search matched Smith"
|
||||
|
||||
echo ""
|
||||
echo "[14/${TOTAL_STEPS}] Verifying department and status filter (no text query)"
|
||||
resp="$(request GET "${BASE_URL}/api/v1/analytics/patients?department=ICU&status=ACTIVE&pageSize=100")"
|
||||
assert_status "200" "${resp}"
|
||||
if ! jq -e --arg enc "${encounter_a}" '.data.data[] | select(.encounterId == $enc)' "${resp}" >/dev/null; then
|
||||
echo "Department/status filter did not return encounter ${encounter_a}"
|
||||
echo "Response body:"
|
||||
cat "${resp}"
|
||||
echo
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: ICU + ACTIVE filter returned expected encounter"
|
||||
|
||||
echo ""
|
||||
echo "[15/${TOTAL_STEPS}] Verifying openAlertCount increments after alert.generated"
|
||||
open_after="$(es_encounter_source "${encounter_a}" | jq -r '.openAlertCount')"
|
||||
if [[ "${open_after}" != "1" ]]; then
|
||||
echo "Expected openAlertCount=1 after critical alert, got ${open_after}"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: openAlertCount incremented to 1"
|
||||
|
||||
echo ""
|
||||
echo "[16/${TOTAL_STEPS}] Verifying alert summary by department"
|
||||
summary_url="${BASE_URL}/api/v1/analytics/alerts/summary?department=ICU"
|
||||
resp="$(request GET "${summary_url}")"
|
||||
assert_status "200" "${resp}"
|
||||
if ! jq -e '.data.summary[] | select(.department == "ICU" and (.total | tonumber) >= 1)' "${resp}" >/dev/null; then
|
||||
echo "Alert summary did not include ICU with total >= 1"
|
||||
echo "Response body:"
|
||||
cat "${resp}"
|
||||
echo
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: alert summary includes ICU department"
|
||||
|
||||
echo ""
|
||||
echo "[17/${TOTAL_STEPS}] Verifying population endpoint validates required code"
|
||||
resp="$(request GET "${BASE_URL}/api/v1/analytics/population?threshold=100&direction=above")"
|
||||
assert_status "400" "${resp}"
|
||||
if [[ "$(jq -r '.error.code' "${resp}")" != "MISSING_CODE" ]]; then
|
||||
echo "Expected MISSING_CODE for population without code parameter"
|
||||
exit 1
|
||||
fi
|
||||
echo "OK: missing code returns 400 MISSING_CODE"
|
||||
|
||||
echo ""
|
||||
echo "All ${TOTAL_STEPS} Elasticsearch + analytics checks passed."
|
||||
echo ""
|
||||
echo "Note: Full index replay (delete indices, reset es-indexer offsets, restart API) is documented"
|
||||
echo "in docs/plans/phase-4-plan.md Step 7 and must be run manually to complete the replay checklist item."
|
||||
Reference in New Issue
Block a user