feature: Optional OCR-Assisted Draft Pre-Fill
This commit is contained in:
@@ -0,0 +1,216 @@
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using System.Text.Json;
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using Microsoft.EntityFrameworkCore;
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using Microsoft.Extensions.Options;
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/// <summary>
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/// Polls for uploaded batches without OCR results and pre-fills draft fields.
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/// OCR is opt-in and non-blocking: failures leave the batch in UPLOADED status
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/// for manual entry.
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/// </summary>
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public class OcrProcessingService : BackgroundService
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{
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private readonly IServiceScopeFactory _scopeFactory;
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private readonly OcrOptions _options;
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private readonly ILogger<OcrProcessingService> _logger;
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public OcrProcessingService(
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IServiceScopeFactory scopeFactory,
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IOptions<OcrOptions> options,
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ILogger<OcrProcessingService> logger)
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{
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_scopeFactory = scopeFactory;
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_options = options.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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_logger.LogInformation(
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"OcrProcessingService started. Provider: {Provider}, poll interval: {PollInterval}s, confidence threshold: {Threshold}",
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_options.Provider,
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_options.PollIntervalSeconds,
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_options.ConfidenceThreshold);
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while (!stoppingToken.IsCancellationRequested)
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{
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try
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{
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await ProcessPendingBatchesAsync(stoppingToken);
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}
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catch (OperationCanceledException) when (stoppingToken.IsCancellationRequested)
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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, "OCR processing cycle failed");
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}
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await Task.Delay(
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TimeSpan.FromSeconds(_options.PollIntervalSeconds), stoppingToken);
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}
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_logger.LogInformation("OcrProcessingService stopped");
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}
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private async Task ProcessPendingBatchesAsync(CancellationToken ct)
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{
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using var scope = _scopeFactory.CreateScope();
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var db = scope.ServiceProvider.GetRequiredService<AppDbContext>();
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var ocr = scope.ServiceProvider.GetRequiredService<IOcrService>();
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var storage = scope.ServiceProvider.GetRequiredService<IDocumentStorageService>();
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var preFiller = scope.ServiceProvider.GetRequiredService<OcrDraftPreFiller>();
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var pendingBatches = await db.DigitizationBatches
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.AsNoTracking()
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.Where(b => b.Status == BatchStatus.Uploaded)
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.Where(b => !db.OcrResults.Any(o => o.BatchId == b.Id))
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.Where(b => !db.DigitizationEvents.Any(e =>
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e.BatchId == b.Id &&
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(e.EventType == DigitizationEventType.OcrCompleted ||
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e.EventType == DigitizationEventType.OcrFailed)))
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.OrderBy(b => b.CreatedAt)
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.Take(5)
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.ToListAsync(ct);
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foreach (var batch in pendingBatches)
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{
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await ProcessBatchAsync(db, ocr, storage, preFiller, batch, ct);
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}
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}
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private async Task ProcessBatchAsync(
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AppDbContext db,
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IOcrService ocr,
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IDocumentStorageService storage,
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OcrDraftPreFiller preFiller,
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DigitizationBatch batch,
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CancellationToken ct)
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{
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var currentStatus = await db.DigitizationBatches
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.AsNoTracking()
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.Where(b => b.Id == batch.Id)
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.Select(b => b.Status)
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.FirstOrDefaultAsync(ct);
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if (currentStatus != BatchStatus.Uploaded)
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{
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_logger.LogDebug(
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"Skipping OCR for batch {BatchId}: status is {Status}",
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batch.Id, currentStatus.ToDbString());
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return;
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}
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var actorUserId = await db.DigitizationEvents
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.AsNoTracking()
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.Where(e => e.BatchId == batch.Id &&
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(e.EventType == DigitizationEventType.Uploaded ||
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e.EventType == DigitizationEventType.CorrectionUploaded))
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.OrderBy(e => e.OccurredAt)
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.Select(e => e.ActorUserId)
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.FirstOrDefaultAsync(ct);
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if (actorUserId == Guid.Empty)
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{
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_logger.LogWarning(
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"Skipping OCR for batch {BatchId}: no upload event found",
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batch.Id);
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return;
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}
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var document = await db.ScannedDocuments
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.AsNoTracking()
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.FirstOrDefaultAsync(d => d.BatchId == batch.Id, ct);
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if (document is null)
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{
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_logger.LogWarning(
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"Skipping OCR for batch {BatchId}: scanned document metadata not found",
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batch.Id);
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return;
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}
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var startedAt = DateTimeOffset.UtcNow;
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db.DigitizationEvents.Add(new DigitizationEvent
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{
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Id = Guid.NewGuid(),
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BatchId = batch.Id,
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EventType = DigitizationEventType.OcrStarted,
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ActorUserId = actorUserId,
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OccurredAt = startedAt,
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MetadataJson = JsonSerializer.Serialize(new
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{
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provider = _options.Provider
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})
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});
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await db.SaveChangesAsync(ct);
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try
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{
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await using var documentStream = await storage.DownloadAsync(document.ObjectKey);
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var extraction = await ocr.ExtractAsync(documentStream, document.ContentType);
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await preFiller.PreFillAsync(batch.Id, batch.BatchType, extraction);
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var fieldConfidences = extraction.Fields
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.GroupBy(f => f.FieldName, StringComparer.Ordinal)
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.ToDictionary(g => g.Key, g => g.First().Confidence, StringComparer.Ordinal);
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var processedAt = DateTimeOffset.UtcNow;
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db.OcrResults.Add(new OcrResult
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{
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Id = Guid.NewGuid(),
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BatchId = batch.Id,
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Provider = _options.Provider,
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FieldConfidencesJson = JsonSerializer.Serialize(fieldConfidences),
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RawText = extraction.RawText,
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DurationMs = extraction.DurationMs,
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ProcessedAt = processedAt
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});
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db.DigitizationEvents.Add(new DigitizationEvent
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{
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Id = Guid.NewGuid(),
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BatchId = batch.Id,
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EventType = DigitizationEventType.OcrCompleted,
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ActorUserId = actorUserId,
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OccurredAt = processedAt,
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MetadataJson = JsonSerializer.Serialize(new
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{
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provider = _options.Provider,
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durationMs = extraction.DurationMs,
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fieldCount = extraction.Fields.Count,
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confidentFieldCount = fieldConfidences.Count(kv => kv.Value >= _options.ConfidenceThreshold)
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})
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});
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await db.SaveChangesAsync(ct);
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_logger.LogInformation(
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"OCR completed for batch {BatchId}: provider={Provider}, fields={FieldCount}, duration={DurationMs}ms",
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batch.Id, _options.Provider, extraction.Fields.Count, extraction.DurationMs);
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}
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catch (Exception ex) when (ex is not OperationCanceledException)
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{
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db.DigitizationEvents.Add(new DigitizationEvent
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{
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Id = Guid.NewGuid(),
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BatchId = batch.Id,
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EventType = DigitizationEventType.OcrFailed,
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ActorUserId = actorUserId,
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OccurredAt = DateTimeOffset.UtcNow,
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MetadataJson = JsonSerializer.Serialize(new
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{
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provider = _options.Provider,
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error = ex.Message
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})
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});
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await db.SaveChangesAsync(ct);
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_logger.LogWarning(
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ex,
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"OCR failed for batch {BatchId}: {ErrorMessage}",
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batch.Id, ex.Message);
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}
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}
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}
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@@ -0,0 +1,5 @@
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public class AzureOcrOptions
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{
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public string Endpoint { get; set; } = "";
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public string ApiKey { get; set; } = "";
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}
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@@ -0,0 +1,12 @@
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public class OcrOptions
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{
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public const string Section = "Ocr";
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public bool Enabled { get; set; } = false;
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public string Provider { get; set; } = "azure"; // "azure" or "tesseract"
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public double ConfidenceThreshold { get; set; } = 0.7;
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public int PollIntervalSeconds { get; set; } = 15;
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public AzureOcrOptions Azure { get; set; } = new();
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public TesseractOcrOptions Tesseract { get; set; } = new();
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}
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@@ -0,0 +1,5 @@
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public class TesseractOcrOptions
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{
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public string DataPath { get; set; } = "/usr/share/tessdata";
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public string Language { get; set; } = "eng";
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}
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@@ -25,7 +25,7 @@ public class FhirEncounterController : ControllerBase
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}
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/// <summary>
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/// FHIR search: GET /fhir/Encounter?patient=X&status=Y&date=Z
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/// FHIR search: GET /fhir/Encounter?patient=X&status=Y&date=Z
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/// Supports search by patient reference, status, and date range.
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/// </summary>
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[HttpGet]
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@@ -25,7 +25,7 @@ public class FhirObservationController : ControllerBase
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}
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/// <summary>
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/// FHIR search: GET /fhir/Observation?patient=X&code=Y&date=Z&category=W
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/// FHIR search: GET /fhir/Observation?patient=X&code=Y&date=Z&category=W
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/// Supports search by patient reference, LOINC code, date range, and category.
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/// </summary>
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[HttpGet]
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@@ -29,7 +29,7 @@ public class FhirPatientController : ControllerBase
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}
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/// <summary>
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/// FHIR search: GET /fhir/Patient?name=X&birthdate=Y&identifier=Z
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/// FHIR search: GET /fhir/Patient?name=X&birthdate=Y&identifier=Z
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/// Supports search by name (contains), birthdate (exact), and MRN identifier.
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/// Returns a FHIR Bundle of type searchset.
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/// </summary>
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@@ -24,6 +24,7 @@ public class AppDbContext : DbContext
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public DbSet<LiveObservation> LiveObservations => Set<LiveObservation>();
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public DbSet<PromotionAttempt> PromotionAttempts => Set<PromotionAttempt>();
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public DbSet<CoverSheet> CoverSheets => Set<CoverSheet>();
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public DbSet<OcrResult> OcrResults => Set<OcrResult>();
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protected override void OnModelCreating(ModelBuilder modelBuilder)
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{
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@@ -8,7 +8,7 @@ public class DigitizationEventConfiguration : IEntityTypeConfiguration<Digitizat
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builder.ToTable("digitization_events", t =>
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{
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t.HasCheckConstraint("chk_digitization_events_event_type",
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"event_type IN ('uploaded', 'entry_started', 'submitted_for_verification', 'rejected', 'verified', 'verified_pending_clinical', 'awaiting_clinical_approval', 'approved', 'promoted', 'live_capture_attested', 'correction_requested', 'verification_failed', 'superseded', 'correction_promoted', 'correction_uploaded', 'promotion_retry_succeeded', 'promotion_retry_failed', 'promotion_retry_exhausted', 'promotion_failed', 'document_accessed', 'cancelled', 'draft_field_updated', 'draft_observation_deleted')");
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"event_type IN ('uploaded', 'entry_started', 'submitted_for_verification', 'rejected', 'verified', 'verified_pending_clinical', 'awaiting_clinical_approval', 'approved', 'promoted', 'live_capture_attested', 'correction_requested', 'verification_failed', 'superseded', 'correction_promoted', 'correction_uploaded', 'promotion_retry_succeeded', 'promotion_retry_failed', 'promotion_retry_exhausted', 'promotion_failed', 'document_accessed', 'cancelled', 'draft_field_updated', 'draft_observation_deleted', 'ocr_started', 'ocr_completed', 'ocr_failed')");
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});
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builder.HasKey(e => e.Id);
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builder.Property(e => e.Id).HasColumnName("id").HasDefaultValueSql("gen_random_uuid()");
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@@ -0,0 +1,24 @@
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using Microsoft.EntityFrameworkCore;
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using Microsoft.EntityFrameworkCore.Metadata.Builders;
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public class OcrResultConfiguration : IEntityTypeConfiguration<OcrResult>
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{
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public void Configure(EntityTypeBuilder<OcrResult> builder)
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{
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builder.ToTable("ocr_results");
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builder.HasKey(o => o.Id);
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builder.Property(o => o.Id).HasColumnName("id").HasDefaultValueSql("gen_random_uuid()");
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builder.Property(o => o.BatchId).HasColumnName("batch_id").IsRequired();
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builder.Property(o => o.Provider).HasColumnName("provider").HasMaxLength(20).IsRequired();
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builder.Property(o => o.FieldConfidencesJson).HasColumnName("field_confidences_json").HasColumnType("jsonb").IsRequired();
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builder.Property(o => o.RawText).HasColumnName("raw_text");
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builder.Property(o => o.DurationMs).HasColumnName("duration_ms").IsRequired();
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builder.Property(o => o.ProcessedAt).HasColumnName("processed_at").HasDefaultValueSql("NOW()");
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builder.HasIndex(o => o.BatchId).IsUnique();
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builder.HasOne(o => o.Batch)
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.WithOne()
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.HasForeignKey<OcrResult>(o => o.BatchId)
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.OnDelete(DeleteBehavior.Restrict);
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}
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}
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+1628
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,69 @@
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using System;
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using Microsoft.EntityFrameworkCore.Migrations;
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#nullable disable
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namespace VigilCareRecordsAPI.Data.Migrations
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{
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/// <inheritdoc />
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public partial class AddOcrResult : Migration
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{
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/// <inheritdoc />
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protected override void Up(MigrationBuilder migrationBuilder)
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{
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migrationBuilder.DropCheckConstraint(
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name: "chk_digitization_events_event_type",
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table: "digitization_events");
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migrationBuilder.CreateTable(
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name: "ocr_results",
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columns: table => new
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{
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id = table.Column<Guid>(type: "uuid", nullable: false, defaultValueSql: "gen_random_uuid()"),
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batch_id = table.Column<Guid>(type: "uuid", nullable: false),
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provider = table.Column<string>(type: "character varying(20)", maxLength: 20, nullable: false),
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field_confidences_json = table.Column<string>(type: "jsonb", nullable: false),
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raw_text = table.Column<string>(type: "text", nullable: true),
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duration_ms = table.Column<int>(type: "integer", nullable: false),
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processed_at = table.Column<DateTimeOffset>(type: "timestamp with time zone", nullable: false, defaultValueSql: "NOW()")
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},
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constraints: table =>
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{
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table.PrimaryKey("PK_ocr_results", x => x.id);
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table.ForeignKey(
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name: "FK_ocr_results_digitization_batches_batch_id",
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column: x => x.batch_id,
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principalTable: "digitization_batches",
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principalColumn: "id",
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onDelete: ReferentialAction.Restrict);
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});
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migrationBuilder.AddCheckConstraint(
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name: "chk_digitization_events_event_type",
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table: "digitization_events",
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sql: "event_type IN ('uploaded', 'entry_started', 'submitted_for_verification', 'rejected', 'verified', 'verified_pending_clinical', 'awaiting_clinical_approval', 'approved', 'promoted', 'live_capture_attested', 'correction_requested', 'verification_failed', 'superseded', 'correction_promoted', 'correction_uploaded', 'promotion_retry_succeeded', 'promotion_retry_failed', 'promotion_retry_exhausted', 'promotion_failed', 'document_accessed', 'cancelled', 'draft_field_updated', 'draft_observation_deleted', 'ocr_started', 'ocr_completed', 'ocr_failed')");
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migrationBuilder.CreateIndex(
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name: "IX_ocr_results_batch_id",
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table: "ocr_results",
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column: "batch_id",
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unique: true);
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}
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/// <inheritdoc />
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protected override void Down(MigrationBuilder migrationBuilder)
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{
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migrationBuilder.DropTable(
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name: "ocr_results");
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migrationBuilder.DropCheckConstraint(
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name: "chk_digitization_events_event_type",
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table: "digitization_events");
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migrationBuilder.AddCheckConstraint(
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name: "chk_digitization_events_event_type",
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table: "digitization_events",
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sql: "event_type IN ('uploaded', 'entry_started', 'submitted_for_verification', 'rejected', 'verified', 'verified_pending_clinical', 'awaiting_clinical_approval', 'approved', 'promoted', 'live_capture_attested', 'correction_requested', 'verification_failed', 'superseded', 'correction_promoted', 'correction_uploaded', 'promotion_retry_succeeded', 'promotion_retry_failed', 'promotion_retry_exhausted', 'promotion_failed', 'document_accessed', 'cancelled', 'draft_field_updated', 'draft_observation_deleted')");
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}
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}
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}
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@@ -476,7 +476,7 @@ namespace VigilCareRecordsAPI.Data.Migrations
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b.ToTable("digitization_events", null, t =>
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{
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t.HasCheckConstraint("chk_digitization_events_event_type", "event_type IN ('uploaded', 'entry_started', 'submitted_for_verification', 'rejected', 'verified', 'verified_pending_clinical', 'awaiting_clinical_approval', 'approved', 'promoted', 'live_capture_attested', 'correction_requested', 'verification_failed', 'superseded', 'correction_promoted', 'correction_uploaded', 'promotion_retry_succeeded', 'promotion_retry_failed', 'promotion_retry_exhausted', 'promotion_failed', 'document_accessed', 'cancelled', 'draft_field_updated', 'draft_observation_deleted')");
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t.HasCheckConstraint("chk_digitization_events_event_type", "event_type IN ('uploaded', 'entry_started', 'submitted_for_verification', 'rejected', 'verified', 'verified_pending_clinical', 'awaiting_clinical_approval', 'approved', 'promoted', 'live_capture_attested', 'correction_requested', 'verification_failed', 'superseded', 'correction_promoted', 'correction_uploaded', 'promotion_retry_succeeded', 'promotion_retry_failed', 'promotion_retry_exhausted', 'promotion_failed', 'document_accessed', 'cancelled', 'draft_field_updated', 'draft_observation_deleted', 'ocr_started', 'ocr_completed', 'ocr_failed')");
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});
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});
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@@ -1007,6 +1007,51 @@ namespace VigilCareRecordsAPI.Data.Migrations
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b.ToTable("observations", "clinical");
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});
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modelBuilder.Entity("OcrResult", b =>
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{
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b.Property<Guid>("Id")
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.ValueGeneratedOnAdd()
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.HasColumnType("uuid")
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.HasColumnName("id")
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.HasDefaultValueSql("gen_random_uuid()");
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b.Property<Guid>("BatchId")
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.HasColumnType("uuid")
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.HasColumnName("batch_id");
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b.Property<int>("DurationMs")
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.HasColumnType("integer")
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.HasColumnName("duration_ms");
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b.Property<string>("FieldConfidencesJson")
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.IsRequired()
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.HasColumnType("jsonb")
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.HasColumnName("field_confidences_json");
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|
||||
b.Property<DateTimeOffset>("ProcessedAt")
|
||||
.ValueGeneratedOnAdd()
|
||||
.HasColumnType("timestamp with time zone")
|
||||
.HasColumnName("processed_at")
|
||||
.HasDefaultValueSql("NOW()");
|
||||
|
||||
b.Property<string>("Provider")
|
||||
.IsRequired()
|
||||
.HasMaxLength(20)
|
||||
.HasColumnType("character varying(20)")
|
||||
.HasColumnName("provider");
|
||||
|
||||
b.Property<string>("RawText")
|
||||
.HasColumnType("text")
|
||||
.HasColumnName("raw_text");
|
||||
|
||||
b.HasKey("Id");
|
||||
|
||||
b.HasIndex("BatchId")
|
||||
.IsUnique();
|
||||
|
||||
b.ToTable("ocr_results", (string)null);
|
||||
});
|
||||
|
||||
modelBuilder.Entity("OutboxEvent", b =>
|
||||
{
|
||||
b.Property<Guid>("Id")
|
||||
@@ -1506,6 +1551,17 @@ namespace VigilCareRecordsAPI.Data.Migrations
|
||||
b.Navigation("Patient");
|
||||
});
|
||||
|
||||
modelBuilder.Entity("OcrResult", b =>
|
||||
{
|
||||
b.HasOne("DigitizationBatch", "Batch")
|
||||
.WithOne()
|
||||
.HasForeignKey("OcrResult", "BatchId")
|
||||
.OnDelete(DeleteBehavior.Restrict)
|
||||
.IsRequired();
|
||||
|
||||
b.Navigation("Batch");
|
||||
});
|
||||
|
||||
modelBuilder.Entity("PromotionAttempt", b =>
|
||||
{
|
||||
b.HasOne("DigitizationBatch", "Batch")
|
||||
|
||||
@@ -0,0 +1,12 @@
|
||||
public class OcrResult
|
||||
{
|
||||
public Guid Id { get; set; }
|
||||
public Guid BatchId { get; set; }
|
||||
public string Provider { get; set; } = null!; // "azure" or "tesseract"
|
||||
public string FieldConfidencesJson { get; set; } = null!; // serialized Dictionary<string, double>
|
||||
public string? RawText { get; set; }
|
||||
public int DurationMs { get; set; }
|
||||
public DateTimeOffset ProcessedAt { get; set; }
|
||||
|
||||
public DigitizationBatch Batch { get; set; } = null!;
|
||||
}
|
||||
@@ -22,7 +22,10 @@ public enum DigitizationEventType
|
||||
DocumentAccessed,
|
||||
Cancelled,
|
||||
DraftFieldUpdated,
|
||||
DraftObservationDeleted
|
||||
DraftObservationDeleted,
|
||||
OcrStarted,
|
||||
OcrCompleted,
|
||||
OcrFailed
|
||||
}
|
||||
|
||||
public static class DigitizationEventTypeExtensions
|
||||
@@ -52,6 +55,9 @@ public static class DigitizationEventTypeExtensions
|
||||
DigitizationEventType.Cancelled => "cancelled",
|
||||
DigitizationEventType.DraftFieldUpdated => "draft_field_updated",
|
||||
DigitizationEventType.DraftObservationDeleted => "draft_observation_deleted",
|
||||
DigitizationEventType.OcrStarted => "ocr_started",
|
||||
DigitizationEventType.OcrCompleted => "ocr_completed",
|
||||
DigitizationEventType.OcrFailed => "ocr_failed",
|
||||
_ => throw new ArgumentOutOfRangeException(nameof(t))
|
||||
};
|
||||
|
||||
@@ -80,6 +86,9 @@ public static class DigitizationEventTypeExtensions
|
||||
"cancelled" => DigitizationEventType.Cancelled,
|
||||
"draft_field_updated" => DigitizationEventType.DraftFieldUpdated,
|
||||
"draft_observation_deleted" => DigitizationEventType.DraftObservationDeleted,
|
||||
"ocr_started" => DigitizationEventType.OcrStarted,
|
||||
"ocr_completed" => DigitizationEventType.OcrCompleted,
|
||||
"ocr_failed" => DigitizationEventType.OcrFailed,
|
||||
_ => throw new ArgumentOutOfRangeException(nameof(v), $"Unknown digitization event type: '{v}'")
|
||||
};
|
||||
}
|
||||
@@ -2,7 +2,8 @@ public record DraftPayloadResponse(
|
||||
Guid BatchId,
|
||||
string Status,
|
||||
string BatchType,
|
||||
BatchTypeFieldRequirements FieldRequirements,
|
||||
BatchTypeFieldRequirements FieldRequirements,
|
||||
OcrConfidenceMap? OcrConfidence,
|
||||
DraftPatientDto? Patient,
|
||||
DraftEncounterDto? Encounter,
|
||||
List<DraftObservationDto> Observations
|
||||
|
||||
@@ -0,0 +1,6 @@
|
||||
public record OcrConfidenceMap(
|
||||
string Provider,
|
||||
DateTimeOffset ProcessedAt,
|
||||
int DurationMs,
|
||||
Dictionary<string, double> FieldConfidences
|
||||
);
|
||||
@@ -0,0 +1,5 @@
|
||||
public record OcrExtractedField(
|
||||
string FieldName, // e.g. "patient.fullName", "observation.HEART_RATE.value"
|
||||
string RawValue, // raw text as extracted
|
||||
double Confidence // 0.0 – 1.0
|
||||
);
|
||||
@@ -0,0 +1,5 @@
|
||||
public record OcrExtractionResult(
|
||||
List<OcrExtractedField> Fields,
|
||||
string RawText,
|
||||
int DurationMs
|
||||
);
|
||||
@@ -2,29 +2,30 @@
|
||||
/// Aggregate work queue health metrics for the supervisor dashboard.
|
||||
/// Returned by GET /api/v1/work-queue/overview.
|
||||
/// </summary>
|
||||
public record WorkQueueOverviewResponse(
|
||||
public record WorkQueueOverviewResponse
|
||||
{
|
||||
/// <summary>
|
||||
/// Count of batches per status. Key is the DB status string
|
||||
/// (e.g. "UPLOADED", "IN_ENTRY", "PENDING_VERIFICATION").
|
||||
/// All 8 statuses are always present, even if count is 0.
|
||||
/// </summary>
|
||||
Dictionary<string, int> StatusCounts,
|
||||
public required Dictionary<string, int> StatusCounts { get; init; }
|
||||
|
||||
/// <summary>
|
||||
/// Average time in minutes that batches currently in PendingVerification
|
||||
/// have been waiting. Zero if no batches are pending.
|
||||
/// </summary>
|
||||
double AverageTimeInQueueMinutes,
|
||||
public required double AverageTimeInQueueMinutes { get; init; }
|
||||
|
||||
/// <summary>
|
||||
/// Rejection rate as a decimal (0.0 to 1.0). Calculated as
|
||||
/// rejections / (rejections + verifications) over the last 24 hours.
|
||||
/// </summary>
|
||||
double RejectRate,
|
||||
public required double RejectRate { get; init; }
|
||||
|
||||
/// <summary>
|
||||
/// Age in minutes of the oldest batch in PendingVerification status.
|
||||
/// Zero if no batches are pending.
|
||||
/// </summary>
|
||||
double OldestPendingVerificationMinutes
|
||||
);
|
||||
public required double OldestPendingVerificationMinutes { get; init; }
|
||||
}
|
||||
|
||||
@@ -53,6 +53,23 @@ try
|
||||
|
||||
builder.Services.Configure<FhirOptions>(builder.Configuration.GetSection(FhirOptions.Section));
|
||||
|
||||
builder.Services.Configure<OcrOptions>(builder.Configuration.GetSection(OcrOptions.Section));
|
||||
|
||||
var ocrOptions = builder.Configuration.GetSection(OcrOptions.Section).Get<OcrOptions>();
|
||||
|
||||
if (ocrOptions?.Enabled == true)
|
||||
{
|
||||
builder.Services.AddSingleton<ImagePreprocessor>();
|
||||
|
||||
if (ocrOptions.Provider == "azure")
|
||||
builder.Services.AddScoped<IOcrService, AzureDocumentOcrService>();
|
||||
else
|
||||
builder.Services.AddScoped<IOcrService, TesseractOcrService>();
|
||||
|
||||
builder.Services.AddScoped<OcrDraftPreFiller>();
|
||||
builder.Services.AddHostedService<OcrProcessingService>();
|
||||
}
|
||||
|
||||
// JWT Authentication
|
||||
var jwtOptions = builder.Configuration.GetSection(JwtOptions.Section).Get<JwtOptions>()!;
|
||||
|
||||
|
||||
@@ -58,6 +58,18 @@ public class DocumentStorageService : IDocumentStorageService
|
||||
.WithExpiry(_options.PresignedUrlExpiryMinutes * 60));
|
||||
}
|
||||
|
||||
public async Task<Stream> DownloadAsync(string objectKey)
|
||||
{
|
||||
var memStream = new MemoryStream();
|
||||
await _minio.GetObjectAsync(new GetObjectArgs()
|
||||
.WithBucket(_options.BucketName)
|
||||
.WithObject(objectKey)
|
||||
.WithCallbackStream(stream => stream.CopyTo(memStream)));
|
||||
|
||||
memStream.Position = 0;
|
||||
return memStream;
|
||||
}
|
||||
|
||||
private async Task EnsureBucketAsync()
|
||||
{
|
||||
var exists = await _minio.BucketExistsAsync(new BucketExistsArgs().WithBucket(_options.BucketName));
|
||||
|
||||
@@ -31,11 +31,29 @@ public class DraftService : IDraftService
|
||||
if (batch is null)
|
||||
throw new NotFoundException("Batch not found.", "BATCH_NOT_FOUND");
|
||||
|
||||
var ocrResult = await _db.OcrResults
|
||||
.AsNoTracking()
|
||||
.FirstOrDefaultAsync(o => o.BatchId == batchId);
|
||||
|
||||
OcrConfidenceMap? ocrConfidence = null;
|
||||
if (ocrResult is not null)
|
||||
{
|
||||
var fieldConfidences = JsonSerializer.Deserialize<Dictionary<string, double>>(
|
||||
ocrResult.FieldConfidencesJson) ?? new Dictionary<string, double>();
|
||||
|
||||
ocrConfidence = new OcrConfidenceMap(
|
||||
ocrResult.Provider,
|
||||
ocrResult.ProcessedAt,
|
||||
ocrResult.DurationMs,
|
||||
fieldConfidences);
|
||||
}
|
||||
|
||||
return new DraftPayloadResponse(
|
||||
batch.Id,
|
||||
batch.Status.ToDbString(),
|
||||
batch.BatchType.ToDbString(),
|
||||
BatchTypeFieldRequirements.ForBatchType(batch.BatchType),
|
||||
ocrConfidence,
|
||||
batch.DraftPatient is not null ? MapPatient(batch.DraftPatient) : null,
|
||||
batch.DraftEncounter is not null ? MapEncounter(batch.DraftEncounter) : null,
|
||||
batch.DraftObservations.Select(MapObservation).OrderBy(o => o.RecordedAt).ToList()
|
||||
|
||||
@@ -22,7 +22,7 @@ public class IdempotencyService : IIdempotencyService
|
||||
return record;
|
||||
}
|
||||
|
||||
public async Task SaveAsync(string idempotencyKey, string operationName, Guid resourceId,
|
||||
public Task SaveAsync(string idempotencyKey, string operationName, Guid resourceId,
|
||||
int httpStatusCode, object responseBody, TimeSpan? ttl = null)
|
||||
{
|
||||
var effectiveTtl = ttl ?? DefaultTtl;
|
||||
@@ -46,5 +46,6 @@ public class IdempotencyService : IIdempotencyService
|
||||
|
||||
_db.IdempotencyRecords.Add(record);
|
||||
// SaveChanges is called by the caller (within the same transaction)
|
||||
return Task.CompletedTask;
|
||||
}
|
||||
}
|
||||
@@ -2,4 +2,5 @@ public interface IDocumentStorageService
|
||||
{
|
||||
Task<(string objectKey, string sha256, long fileSize)> UploadAsync(Stream fileStream, string contentType, Guid batchId);
|
||||
Task<string> GetPresignedUrlAsync(string objectKey);
|
||||
Task<Stream> DownloadAsync(string objectKey);
|
||||
}
|
||||
@@ -0,0 +1,4 @@
|
||||
public interface IOcrService
|
||||
{
|
||||
Task<OcrExtractionResult> ExtractAsync(Stream documentStream, string contentType);
|
||||
}
|
||||
@@ -0,0 +1,264 @@
|
||||
using Azure;
|
||||
using Azure.AI.DocumentIntelligence;
|
||||
using Microsoft.Extensions.Options;
|
||||
|
||||
public class AzureDocumentOcrService : IOcrService
|
||||
{
|
||||
private const double DefaultTableConfidence = 0.75;
|
||||
|
||||
private static readonly Dictionary<string, string> ClinicalLabelMap =
|
||||
new(StringComparer.OrdinalIgnoreCase)
|
||||
{
|
||||
["patient name"] = "patient.fullName",
|
||||
["name"] = "patient.fullName",
|
||||
["full name"] = "patient.fullName",
|
||||
["date of birth"] = "patient.dateOfBirth",
|
||||
["dob"] = "patient.dateOfBirth",
|
||||
["birth date"] = "patient.dateOfBirth",
|
||||
["sex"] = "patient.sex",
|
||||
["gender"] = "patient.sex",
|
||||
["admission date"] = "encounter.admissionDate",
|
||||
["admitted"] = "encounter.admissionDate",
|
||||
["department"] = "encounter.department",
|
||||
["ward"] = "encounter.department",
|
||||
["unit"] = "encounter.department",
|
||||
["room"] = "encounter.roomBed",
|
||||
["bed"] = "encounter.roomBed",
|
||||
["room/bed"] = "encounter.roomBed",
|
||||
["hr"] = "observation.HEART_RATE.value",
|
||||
["heart rate"] = "observation.HEART_RATE.value",
|
||||
["pulse"] = "observation.HEART_RATE.value",
|
||||
["temp"] = "observation.TEMP_C.value",
|
||||
["temperature"] = "observation.TEMP_C.value",
|
||||
["bp sys"] = "observation.BP_SYSTOLIC.value",
|
||||
["systolic"] = "observation.BP_SYSTOLIC.value",
|
||||
["bp dia"] = "observation.BP_DIASTOLIC.value",
|
||||
["diastolic"] = "observation.BP_DIASTOLIC.value",
|
||||
["rr"] = "observation.RESP_RATE.value",
|
||||
["resp rate"] = "observation.RESP_RATE.value",
|
||||
["respiratory rate"] = "observation.RESP_RATE.value",
|
||||
["spo2"] = "observation.SPO2.value",
|
||||
["o2 sat"] = "observation.SPO2.value",
|
||||
["oxygen saturation"] = "observation.SPO2.value",
|
||||
};
|
||||
|
||||
private static readonly HashSet<string> TimestampHeaders = new(StringComparer.OrdinalIgnoreCase)
|
||||
{
|
||||
"time", "date", "datetime", "date/time", "recorded", "recorded at", "timestamp"
|
||||
};
|
||||
|
||||
private static readonly HashSet<string> GenericTableHeaders = new(StringComparer.OrdinalIgnoreCase)
|
||||
{
|
||||
"label", "name", "parameter", "field", "item", "value", "result", "reading"
|
||||
};
|
||||
|
||||
private readonly DocumentIntelligenceClient _client;
|
||||
private readonly ILogger<AzureDocumentOcrService> _logger;
|
||||
|
||||
public AzureDocumentOcrService(
|
||||
IOptions<OcrOptions> options,
|
||||
ILogger<AzureDocumentOcrService> logger)
|
||||
{
|
||||
var opts = options.Value.Azure;
|
||||
_client = new DocumentIntelligenceClient(
|
||||
new Uri(opts.Endpoint),
|
||||
new AzureKeyCredential(opts.ApiKey));
|
||||
_logger = logger;
|
||||
}
|
||||
|
||||
public async Task<OcrExtractionResult> ExtractAsync(
|
||||
Stream documentStream, string contentType)
|
||||
{
|
||||
var sw = System.Diagnostics.Stopwatch.StartNew();
|
||||
|
||||
var content = BinaryData.FromStream(documentStream);
|
||||
var operation = await _client.AnalyzeDocumentAsync(
|
||||
WaitUntil.Completed,
|
||||
"prebuilt-document",
|
||||
content);
|
||||
|
||||
var result = operation.Value;
|
||||
var fields = new List<OcrExtractedField>();
|
||||
|
||||
foreach (var kv in result.KeyValuePairs ?? [])
|
||||
{
|
||||
if (kv.Key?.Content is null || kv.Value?.Content is null) continue;
|
||||
|
||||
var fieldName = MapAzureKeyToFieldName(kv.Key.Content);
|
||||
if (fieldName is null) continue;
|
||||
|
||||
fields.Add(new OcrExtractedField(
|
||||
fieldName,
|
||||
kv.Value.Content,
|
||||
kv.Confidence));
|
||||
}
|
||||
|
||||
foreach (var table in result.Tables ?? [])
|
||||
{
|
||||
fields.AddRange(ExtractTableObservations(table));
|
||||
}
|
||||
|
||||
var rawText = string.Join("\n", (result.Pages ?? [])
|
||||
.SelectMany(p => p.Lines?.Select(l => l.Content) ?? []));
|
||||
|
||||
sw.Stop();
|
||||
return new OcrExtractionResult(fields, rawText, (int)sw.ElapsedMilliseconds);
|
||||
}
|
||||
|
||||
private static string? MapAzureKeyToFieldName(string key)
|
||||
{
|
||||
var normalized = key.Trim();
|
||||
if (normalized.Length == 0)
|
||||
return null;
|
||||
|
||||
return ClinicalLabelMap.GetValueOrDefault(normalized);
|
||||
}
|
||||
|
||||
private static List<OcrExtractedField> ExtractTableObservations(DocumentTable table)
|
||||
{
|
||||
var fields = new List<OcrExtractedField>();
|
||||
if (table.Cells is null || table.Cells.Count == 0)
|
||||
return fields;
|
||||
|
||||
if (table.ColumnCount == 2)
|
||||
{
|
||||
var labelValueFields = ExtractLabelValueTable(table);
|
||||
if (labelValueFields.Count > 0)
|
||||
return labelValueFields;
|
||||
}
|
||||
|
||||
return ExtractGridTable(table);
|
||||
}
|
||||
|
||||
private static List<OcrExtractedField> ExtractLabelValueTable(DocumentTable table)
|
||||
{
|
||||
var fields = new List<OcrExtractedField>();
|
||||
var dataStartRow = HasGenericHeaderRow(table.Cells) ? 1 : 0;
|
||||
|
||||
for (var row = dataStartRow; row < table.RowCount; row++)
|
||||
{
|
||||
var key = GetCellContent(table.Cells, row, 0);
|
||||
var value = GetCellContent(table.Cells, row, 1);
|
||||
if (string.IsNullOrWhiteSpace(key) || string.IsNullOrWhiteSpace(value))
|
||||
continue;
|
||||
|
||||
var fieldName = MapAzureKeyToFieldName(key);
|
||||
if (fieldName is null)
|
||||
continue;
|
||||
|
||||
fields.Add(new OcrExtractedField(fieldName, value.Trim(), DefaultTableConfidence));
|
||||
}
|
||||
|
||||
return fields;
|
||||
}
|
||||
|
||||
private static List<OcrExtractedField> ExtractGridTable(DocumentTable table)
|
||||
{
|
||||
var fields = new List<OcrExtractedField>();
|
||||
var headerCells = table.Cells
|
||||
.Where(c => c.RowIndex == 0)
|
||||
.OrderBy(c => c.ColumnIndex)
|
||||
.ToList();
|
||||
|
||||
if (headerCells.Count == 0)
|
||||
return fields;
|
||||
|
||||
var columnMappings = new Dictionary<int, string?>();
|
||||
foreach (var headerCell in headerCells)
|
||||
{
|
||||
columnMappings[headerCell.ColumnIndex] = MapTableHeader(headerCell.Content);
|
||||
}
|
||||
|
||||
var observationCodes = columnMappings.Values
|
||||
.Where(v => v is not null and not "recordedAt")
|
||||
.Cast<string>()
|
||||
.Distinct()
|
||||
.ToList();
|
||||
|
||||
if (observationCodes.Count == 0)
|
||||
return fields;
|
||||
|
||||
for (var row = 1; row < table.RowCount; row++)
|
||||
{
|
||||
string? recordedAt = null;
|
||||
|
||||
foreach (var cell in table.Cells.Where(c => c.RowIndex == row))
|
||||
{
|
||||
if (!columnMappings.TryGetValue(cell.ColumnIndex, out var mapping)
|
||||
|| mapping is null
|
||||
|| string.IsNullOrWhiteSpace(cell.Content))
|
||||
{
|
||||
continue;
|
||||
}
|
||||
|
||||
var content = cell.Content.Trim();
|
||||
|
||||
if (mapping == "recordedAt")
|
||||
{
|
||||
recordedAt = content;
|
||||
continue;
|
||||
}
|
||||
|
||||
fields.Add(new OcrExtractedField(
|
||||
$"observation.{mapping}.value",
|
||||
content,
|
||||
DefaultTableConfidence));
|
||||
}
|
||||
|
||||
if (recordedAt is null)
|
||||
continue;
|
||||
|
||||
foreach (var code in observationCodes)
|
||||
{
|
||||
fields.Add(new OcrExtractedField(
|
||||
$"observation.{code}.recordedAt",
|
||||
recordedAt,
|
||||
DefaultTableConfidence));
|
||||
}
|
||||
}
|
||||
|
||||
return fields;
|
||||
}
|
||||
|
||||
private static string? MapTableHeader(string? header)
|
||||
{
|
||||
if (string.IsNullOrWhiteSpace(header))
|
||||
return null;
|
||||
|
||||
var normalized = header.Trim();
|
||||
if (TimestampHeaders.Contains(normalized))
|
||||
return "recordedAt";
|
||||
|
||||
var fieldName = MapAzureKeyToFieldName(normalized);
|
||||
if (fieldName is null)
|
||||
return null;
|
||||
|
||||
const string observationPrefix = "observation.";
|
||||
const string valueSuffix = ".value";
|
||||
if (fieldName.StartsWith(observationPrefix, StringComparison.Ordinal)
|
||||
&& fieldName.EndsWith(valueSuffix, StringComparison.Ordinal))
|
||||
{
|
||||
return fieldName[observationPrefix.Length..^valueSuffix.Length];
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
private static bool HasGenericHeaderRow(IReadOnlyList<DocumentTableCell> cells)
|
||||
{
|
||||
var headerCells = cells.Where(c => c.RowIndex == 0).ToList();
|
||||
if (headerCells.Count != 2)
|
||||
return false;
|
||||
|
||||
return headerCells.All(c =>
|
||||
GenericTableHeaders.Contains(c.Content?.Trim() ?? string.Empty));
|
||||
}
|
||||
|
||||
private static string? GetCellContent(
|
||||
IReadOnlyList<DocumentTableCell> cells, int row, int column)
|
||||
{
|
||||
return cells
|
||||
.FirstOrDefault(c => c.RowIndex == row && c.ColumnIndex == column)
|
||||
?.Content;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,66 @@
|
||||
using Docnet.Core;
|
||||
using Docnet.Core.Models;
|
||||
using SixLabors.ImageSharp;
|
||||
using SixLabors.ImageSharp.PixelFormats;
|
||||
using SixLabors.ImageSharp.Processing;
|
||||
|
||||
public class ImagePreprocessor
|
||||
{
|
||||
// US Letter at 300 DPI — sufficient for Tesseract on clinical scans.
|
||||
private const int PdfRenderWidth = 2550;
|
||||
private const int PdfRenderHeight = 3300;
|
||||
|
||||
public Stream Preprocess(Stream input, string contentType)
|
||||
{
|
||||
Stream? pdfRenderStream = null;
|
||||
try
|
||||
{
|
||||
if (contentType == "application/pdf")
|
||||
{
|
||||
pdfRenderStream = RenderPdfFirstPage(input);
|
||||
input = pdfRenderStream;
|
||||
}
|
||||
|
||||
using var image = Image.Load(input);
|
||||
|
||||
image.Mutate(ctx => ctx
|
||||
.Grayscale()
|
||||
.GaussianSharpen(1.5f)
|
||||
.BinaryThreshold(0.5f));
|
||||
|
||||
var output = new MemoryStream();
|
||||
image.SaveAsPng(output);
|
||||
output.Position = 0;
|
||||
return output;
|
||||
}
|
||||
finally
|
||||
{
|
||||
pdfRenderStream?.Dispose();
|
||||
}
|
||||
}
|
||||
|
||||
private static Stream RenderPdfFirstPage(Stream pdfStream)
|
||||
{
|
||||
using var buffer = new MemoryStream();
|
||||
pdfStream.CopyTo(buffer);
|
||||
var pdfBytes = buffer.ToArray();
|
||||
|
||||
using var docReader = DocLib.Instance.GetDocReader(
|
||||
pdfBytes,
|
||||
new PageDimensions(PdfRenderWidth, PdfRenderHeight));
|
||||
|
||||
if (docReader.GetPageCount() == 0)
|
||||
throw new InvalidOperationException("PDF contains no pages.");
|
||||
|
||||
using var pageReader = docReader.GetPageReader(0);
|
||||
var rawBytes = pageReader.GetImage();
|
||||
var width = pageReader.GetPageWidth();
|
||||
var height = pageReader.GetPageHeight();
|
||||
|
||||
using var image = Image.LoadPixelData<Bgra32>(rawBytes, width, height);
|
||||
var output = new MemoryStream();
|
||||
image.SaveAsPng(output);
|
||||
output.Position = 0;
|
||||
return output;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,252 @@
|
||||
using System.Globalization;
|
||||
using System.Text.RegularExpressions;
|
||||
using Microsoft.EntityFrameworkCore;
|
||||
using Microsoft.Extensions.Options;
|
||||
|
||||
public class OcrDraftPreFiller
|
||||
{
|
||||
private static readonly Dictionary<string, string> DefaultUnits = new(StringComparer.Ordinal)
|
||||
{
|
||||
["HEART_RATE"] = "bpm",
|
||||
["TEMP_C"] = "C",
|
||||
["BP_SYSTOLIC"] = "mmHg",
|
||||
["BP_DIASTOLIC"] = "mmHg",
|
||||
["RESP_RATE"] = "breaths/min",
|
||||
["SPO2"] = "%",
|
||||
["POTASSIUM_MEQ_L"] = "mEq/L",
|
||||
["WBC_K_UL"] = "K/uL",
|
||||
["GLUCOSE_MG_DL"] = "mg/dL",
|
||||
["LACTATE_MMOL_L"] = "mmol/L",
|
||||
};
|
||||
|
||||
private static readonly Regex ObservationValueField =
|
||||
new(@"^observation\.([^.]+)\.value$", RegexOptions.Compiled | RegexOptions.CultureInvariant);
|
||||
|
||||
private readonly AppDbContext _db;
|
||||
private readonly OcrOptions _options;
|
||||
private readonly ILogger<OcrDraftPreFiller> _logger;
|
||||
|
||||
public OcrDraftPreFiller(
|
||||
AppDbContext db,
|
||||
IOptions<OcrOptions> options,
|
||||
ILogger<OcrDraftPreFiller> logger)
|
||||
{
|
||||
_db = db;
|
||||
_options = options.Value;
|
||||
_logger = logger;
|
||||
}
|
||||
|
||||
public async Task PreFillAsync(
|
||||
Guid batchId, BatchType batchType, OcrExtractionResult extraction)
|
||||
{
|
||||
var requirements = BatchTypeFieldRequirements.ForBatchType(batchType);
|
||||
var confidentFields = extraction.Fields
|
||||
.Where(f => f.Confidence >= _options.ConfidenceThreshold)
|
||||
.GroupBy(f => f.FieldName, StringComparer.Ordinal)
|
||||
.ToDictionary(g => g.Key, g => g.First(), StringComparer.Ordinal);
|
||||
|
||||
if (requirements.ShowPatientDemographics)
|
||||
await PreFillPatientAsync(batchId, confidentFields);
|
||||
|
||||
if (requirements.ShowEncounterContext)
|
||||
await PreFillEncounterAsync(batchId, confidentFields);
|
||||
|
||||
if (requirements.ShowObservations)
|
||||
await PreFillObservationsAsync(batchId, confidentFields);
|
||||
|
||||
await _db.SaveChangesAsync();
|
||||
}
|
||||
|
||||
private async Task PreFillPatientAsync(
|
||||
Guid batchId, Dictionary<string, OcrExtractedField> fields)
|
||||
{
|
||||
if (!fields.Keys.Any(k => k.StartsWith("patient.", StringComparison.Ordinal)))
|
||||
return;
|
||||
|
||||
var patient = await _db.DraftPatients.FirstOrDefaultAsync(p => p.BatchId == batchId);
|
||||
var now = DateTimeOffset.UtcNow;
|
||||
|
||||
if (patient is null)
|
||||
{
|
||||
patient = new DraftPatient
|
||||
{
|
||||
Id = Guid.NewGuid(),
|
||||
BatchId = batchId,
|
||||
CreatedAt = now,
|
||||
UpdatedAt = now
|
||||
};
|
||||
_db.DraftPatients.Add(patient);
|
||||
}
|
||||
|
||||
if (fields.TryGetValue("patient.fullName", out var name))
|
||||
patient.FullName = name.RawValue.Trim();
|
||||
|
||||
if (fields.TryGetValue("patient.dateOfBirth", out var dob)
|
||||
&& TryParseDate(dob.RawValue, out var parsedDob))
|
||||
patient.DateOfBirth = parsedDob;
|
||||
|
||||
if (fields.TryGetValue("patient.sex", out var sex))
|
||||
patient.Sex = NormalizeSex(sex.RawValue);
|
||||
|
||||
patient.UpdatedAt = now;
|
||||
}
|
||||
|
||||
private async Task PreFillEncounterAsync(
|
||||
Guid batchId, Dictionary<string, OcrExtractedField> fields)
|
||||
{
|
||||
if (!fields.Keys.Any(k => k.StartsWith("encounter.", StringComparison.Ordinal)))
|
||||
return;
|
||||
|
||||
var encounter = await _db.DraftEncounters.FirstOrDefaultAsync(e => e.BatchId == batchId);
|
||||
var now = DateTimeOffset.UtcNow;
|
||||
|
||||
if (encounter is null)
|
||||
{
|
||||
encounter = new DraftEncounter
|
||||
{
|
||||
Id = Guid.NewGuid(),
|
||||
BatchId = batchId,
|
||||
CreatedAt = now,
|
||||
UpdatedAt = now
|
||||
};
|
||||
_db.DraftEncounters.Add(encounter);
|
||||
}
|
||||
|
||||
if (fields.TryGetValue("encounter.admissionDate", out var admissionDate)
|
||||
&& TryParseDateTime(admissionDate.RawValue, out var parsedAdmission))
|
||||
encounter.AdmissionDate = parsedAdmission;
|
||||
|
||||
if (fields.TryGetValue("encounter.department", out var department)
|
||||
&& TryParseDepartment(department.RawValue, out var parsedDepartment))
|
||||
encounter.Department = parsedDepartment;
|
||||
|
||||
if (fields.TryGetValue("encounter.roomBed", out var roomBed))
|
||||
encounter.RoomBed = roomBed.RawValue.Trim();
|
||||
|
||||
if (fields.TryGetValue("encounter.admissionReason", out var admissionReason))
|
||||
encounter.AdmissionReason = admissionReason.RawValue.Trim();
|
||||
|
||||
encounter.UpdatedAt = now;
|
||||
}
|
||||
|
||||
private async Task PreFillObservationsAsync(
|
||||
Guid batchId, Dictionary<string, OcrExtractedField> fields)
|
||||
{
|
||||
var observationCodes = fields.Keys
|
||||
.Select(k => ObservationValueField.Match(k))
|
||||
.Where(m => m.Success)
|
||||
.Select(m => m.Groups[1].Value)
|
||||
.Distinct(StringComparer.Ordinal)
|
||||
.ToList();
|
||||
|
||||
if (observationCodes.Count == 0)
|
||||
return;
|
||||
|
||||
var existingCodes = await _db.DraftObservations
|
||||
.Where(o => o.BatchId == batchId)
|
||||
.Select(o => o.ObservationCode)
|
||||
.ToListAsync();
|
||||
|
||||
var existing = existingCodes.ToHashSet(StringComparer.Ordinal);
|
||||
var now = DateTimeOffset.UtcNow;
|
||||
|
||||
foreach (var code in observationCodes)
|
||||
{
|
||||
if (existing.Contains(code))
|
||||
continue;
|
||||
|
||||
if (!fields.TryGetValue($"observation.{code}.value", out var valueField))
|
||||
continue;
|
||||
|
||||
if (!decimal.TryParse(
|
||||
valueField.RawValue,
|
||||
NumberStyles.Number,
|
||||
CultureInfo.InvariantCulture,
|
||||
out var value)
|
||||
&& !decimal.TryParse(valueField.RawValue, out value))
|
||||
{
|
||||
_logger.LogDebug(
|
||||
"Skipping OCR observation {Code} for batch {BatchId}: unparsable value '{Value}'",
|
||||
code, batchId, valueField.RawValue);
|
||||
continue;
|
||||
}
|
||||
|
||||
if (!PlausibilityValidator.IsPlausible(code, value, out var reason))
|
||||
{
|
||||
_logger.LogDebug(
|
||||
"Skipping OCR observation {Code} for batch {BatchId}: {Reason}",
|
||||
code, batchId, reason);
|
||||
continue;
|
||||
}
|
||||
|
||||
var unit = fields.TryGetValue($"observation.{code}.unit", out var unitField)
|
||||
? unitField.RawValue.Trim()
|
||||
: DefaultUnits.GetValueOrDefault(code, string.Empty);
|
||||
|
||||
var recordedAt = now;
|
||||
if (fields.TryGetValue($"observation.{code}.recordedAt", out var recordedAtField)
|
||||
&& TryParseDateTime(recordedAtField.RawValue, out var parsedRecordedAt))
|
||||
recordedAt = parsedRecordedAt;
|
||||
|
||||
_db.DraftObservations.Add(new DraftObservation
|
||||
{
|
||||
Id = Guid.NewGuid(),
|
||||
BatchId = batchId,
|
||||
ObservationCode = code,
|
||||
Value = value,
|
||||
Unit = unit,
|
||||
RecordedAt = recordedAt,
|
||||
CreatedAt = now
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
private static bool TryParseDate(string raw, out DateOnly result)
|
||||
{
|
||||
if (DateOnly.TryParse(raw.Trim(), CultureInfo.InvariantCulture, DateTimeStyles.None, out result))
|
||||
return true;
|
||||
|
||||
return DateOnly.TryParse(raw.Trim(), out result);
|
||||
}
|
||||
|
||||
private static bool TryParseDateTime(string raw, out DateTimeOffset result)
|
||||
{
|
||||
if (DateTimeOffset.TryParse(raw.Trim(), CultureInfo.InvariantCulture, DateTimeStyles.AssumeUniversal, out result))
|
||||
return true;
|
||||
|
||||
if (TryParseDate(raw, out var dateOnly))
|
||||
{
|
||||
result = new DateTimeOffset(dateOnly.ToDateTime(TimeOnly.MinValue), TimeSpan.Zero);
|
||||
return true;
|
||||
}
|
||||
|
||||
return DateTimeOffset.TryParse(raw.Trim(), out result);
|
||||
}
|
||||
|
||||
private static bool TryParseDepartment(string raw, out Department result)
|
||||
{
|
||||
var trimmed = raw.Trim();
|
||||
if (DepartmentExtensions.TryFromDbString(trimmed, out result))
|
||||
return true;
|
||||
|
||||
foreach (Department department in Enum.GetValues<Department>())
|
||||
{
|
||||
if (department.ToDbString().Equals(trimmed, StringComparison.OrdinalIgnoreCase))
|
||||
{
|
||||
result = department;
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
||||
result = default;
|
||||
return false;
|
||||
}
|
||||
|
||||
private static string NormalizeSex(string raw) =>
|
||||
raw.Trim().ToLowerInvariant() switch
|
||||
{
|
||||
"m" or "male" => "Male",
|
||||
"f" or "female" => "Female",
|
||||
_ => raw.Trim()
|
||||
};
|
||||
}
|
||||
@@ -0,0 +1,90 @@
|
||||
using System.Text.RegularExpressions;
|
||||
using Microsoft.Extensions.Options;
|
||||
using Tesseract;
|
||||
|
||||
public class TesseractOcrService : IOcrService
|
||||
{
|
||||
private static readonly (Regex Pattern, string FieldName)[] ClinicalPatterns =
|
||||
[
|
||||
(new Regex(@"(?:Patient\s+)?Name[:\s]+(.+)", RegexOptions.IgnoreCase | RegexOptions.Multiline), "patient.fullName"),
|
||||
(new Regex(@"DOB[:\s]+(\d{1,2}[/-]\d{1,2}[/-]\d{2,4})", RegexOptions.IgnoreCase), "patient.dateOfBirth"),
|
||||
(new Regex(@"(?:Date of Birth|Birth Date)[:\s]+(\d{1,2}[/-]\d{1,2}[/-]\d{2,4})", RegexOptions.IgnoreCase), "patient.dateOfBirth"),
|
||||
(new Regex(@"(?:Sex|Gender)[:\s]+(\S+)", RegexOptions.IgnoreCase), "patient.sex"),
|
||||
(new Regex(@"(?:Admission Date|Admitted)[:\s]+(\d{1,2}[/-]\d{1,2}[/-]\d{2,4})", RegexOptions.IgnoreCase), "encounter.admissionDate"),
|
||||
(new Regex(@"(?:Department|Ward|Unit)[:\s]+(.+)", RegexOptions.IgnoreCase | RegexOptions.Multiline), "encounter.department"),
|
||||
(new Regex(@"(?:Room(?:/Bed)?|Bed)[:\s]+(.+)", RegexOptions.IgnoreCase | RegexOptions.Multiline), "encounter.roomBed"),
|
||||
(new Regex(@"HR[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.HEART_RATE.value"),
|
||||
(new Regex(@"(?:Heart Rate|Pulse)[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.HEART_RATE.value"),
|
||||
(new Regex(@"(?:Temp|Temperature)[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.TEMP_C.value"),
|
||||
(new Regex(@"(?:BP Sys|Systolic)[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.BP_SYSTOLIC.value"),
|
||||
(new Regex(@"(?:BP Dia|Diastolic)[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.BP_DIASTOLIC.value"),
|
||||
(new Regex(@"(?:RR|Resp(?:iratory)?\s*Rate)[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.RESP_RATE.value"),
|
||||
(new Regex(@"(?:SpO2|O2 Sat)[:\s]+(\d+(?:\.\d+)?)", RegexOptions.IgnoreCase), "observation.SPO2.value"),
|
||||
];
|
||||
|
||||
private readonly TesseractOcrOptions _options;
|
||||
private readonly ImagePreprocessor _preprocessor;
|
||||
private readonly ILogger<TesseractOcrService> _logger;
|
||||
|
||||
public TesseractOcrService(
|
||||
IOptions<OcrOptions> options,
|
||||
ImagePreprocessor preprocessor,
|
||||
ILogger<TesseractOcrService> logger)
|
||||
{
|
||||
_options = options.Value.Tesseract;
|
||||
_preprocessor = preprocessor;
|
||||
_logger = logger;
|
||||
}
|
||||
|
||||
public async Task<OcrExtractionResult> ExtractAsync(
|
||||
Stream documentStream, string contentType)
|
||||
{
|
||||
var sw = System.Diagnostics.Stopwatch.StartNew();
|
||||
|
||||
using var preprocessed = _preprocessor.Preprocess(documentStream, contentType);
|
||||
using var memStream = new MemoryStream();
|
||||
await preprocessed.CopyToAsync(memStream);
|
||||
var imageBytes = memStream.ToArray();
|
||||
|
||||
using var engine = new TesseractEngine(
|
||||
_options.DataPath, _options.Language, EngineMode.Default);
|
||||
using var pix = Pix.LoadFromMemory(imageBytes);
|
||||
using var page = engine.Process(pix);
|
||||
|
||||
var rawText = page.GetText();
|
||||
var meanConfidence = page.GetMeanConfidence();
|
||||
var fields = ParseClinicalText(rawText, meanConfidence);
|
||||
|
||||
sw.Stop();
|
||||
return new OcrExtractionResult(fields, rawText, (int)sw.ElapsedMilliseconds);
|
||||
}
|
||||
|
||||
private static List<OcrExtractedField> ParseClinicalText(string text, float meanConfidence)
|
||||
{
|
||||
var fields = new List<OcrExtractedField>();
|
||||
if (string.IsNullOrWhiteSpace(text))
|
||||
return fields;
|
||||
|
||||
var baseConfidence = Math.Clamp(meanConfidence / 100f, 0.0, 1.0);
|
||||
var matchedFields = new HashSet<string>(StringComparer.Ordinal);
|
||||
|
||||
foreach (var (pattern, fieldName) in ClinicalPatterns)
|
||||
{
|
||||
if (matchedFields.Contains(fieldName))
|
||||
continue;
|
||||
|
||||
var match = pattern.Match(text);
|
||||
if (!match.Success)
|
||||
continue;
|
||||
|
||||
var value = match.Groups[1].Value.Trim();
|
||||
if (value.Length == 0)
|
||||
continue;
|
||||
|
||||
fields.Add(new OcrExtractedField(fieldName, value, baseConfidence));
|
||||
matchedFields.Add(fieldName);
|
||||
}
|
||||
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
@@ -526,7 +526,7 @@ public class PromotionService : IPromotionService
|
||||
return encounter;
|
||||
}
|
||||
|
||||
private async Task<(Guid[] observationIds, int outboxCount)> PromoteObservationsAsync(
|
||||
private Task<(Guid[] observationIds, int outboxCount)> PromoteObservationsAsync(
|
||||
DigitizationBatch batch, Guid patientId, Guid encounterId,
|
||||
bool enableRetroactiveAlerts, DateTimeOffset now)
|
||||
{
|
||||
@@ -600,7 +600,7 @@ public class PromotionService : IPromotionService
|
||||
"{OutboxCount} outbox events (shouldAlert={ShouldAlert}, track={Track})",
|
||||
observationIds.Count, batch.Id, outboxCount, shouldAlert, batch.Track.ToDbString());
|
||||
|
||||
return (observationIds.ToArray(), outboxCount);
|
||||
return Task.FromResult((observationIds.ToArray(), outboxCount));
|
||||
}
|
||||
|
||||
public async Task<PromotionResult> PromoteAsync(Guid batchId, Guid actorUserId)
|
||||
|
||||
@@ -179,10 +179,12 @@ public class WorkQueueService : IWorkQueueService
|
||||
"Work queue overview: {PendingCount} pending, avg queue {AvgMinutes:F1}m, reject rate {RejectRate:P1}",
|
||||
pendingBatches.Count, avgTimeInQueueMinutes, rejectRate);
|
||||
|
||||
return new WorkQueueOverviewResponse(
|
||||
StatusCounts: statusCounts,
|
||||
AverageTimeInQueueMinutes: Math.Round(avgTimeInQueueMinutes, 1),
|
||||
RejectRate: Math.Round(rejectRate, 4),
|
||||
OldestPendingVerificationMinutes: Math.Round(oldestPendingMinutes, 1));
|
||||
return new WorkQueueOverviewResponse
|
||||
{
|
||||
StatusCounts = statusCounts,
|
||||
AverageTimeInQueueMinutes = Math.Round(avgTimeInQueueMinutes, 1),
|
||||
RejectRate = Math.Round(rejectRate, 4),
|
||||
OldestPendingVerificationMinutes = Math.Round(oldestPendingMinutes, 1)
|
||||
};
|
||||
}
|
||||
}
|
||||
@@ -11,7 +11,9 @@
|
||||
<ItemGroup>
|
||||
<PackageReference Include="AspNetCore.HealthChecks.NpgSql" Version="8.0.2" />
|
||||
<PackageReference Include="AspNetCore.HealthChecks.Redis" Version="8.0.1" />
|
||||
<PackageReference Include="Azure.AI.DocumentIntelligence" Version="1.0.0" />
|
||||
<PackageReference Include="BCrypt.Net-Next" Version="4.0.3" />
|
||||
<PackageReference Include="Docnet.Core" Version="2.6.0" />
|
||||
<PackageReference Include="FluentValidation.AspNetCore" Version="11.3.0" />
|
||||
<PackageReference Include="Hl7.Fhir.R4" Version="5.11.2" />
|
||||
<PackageReference Include="Microsoft.AspNetCore.Authentication.JwtBearer" Version="8.0.4" />
|
||||
@@ -28,8 +30,10 @@
|
||||
<PackageReference Include="Serilog.AspNetCore" Version="8.0.2" />
|
||||
<PackageReference Include="Serilog.Sinks.Console" Version="5.0.1" />
|
||||
<PackageReference Include="Serilog.Sinks.Seq" Version="9.1.0" />
|
||||
<PackageReference Include="SixLabors.ImageSharp" Version="3.1.11" />
|
||||
<PackageReference Include="StackExchange.Redis" Version="3.0.0" />
|
||||
<PackageReference Include="Swashbuckle.AspNetCore" Version="6.6.2" />
|
||||
<PackageReference Include="Tesseract" Version="5.2.0" />
|
||||
</ItemGroup>
|
||||
|
||||
</Project>
|
||||
|
||||
@@ -76,5 +76,19 @@
|
||||
"PublisherName": "VigilCare Records",
|
||||
"PublisherUrl": "https://vigilcare.local",
|
||||
"ServerVersion": "1.0.0"
|
||||
},
|
||||
"Ocr": {
|
||||
"Enabled": false,
|
||||
"Provider": "azure",
|
||||
"ConfidenceThreshold": 0.7,
|
||||
"PollIntervalSeconds": 15,
|
||||
"Azure": {
|
||||
"Endpoint": "",
|
||||
"ApiKey": ""
|
||||
},
|
||||
"Tesseract": {
|
||||
"DataPath": "/usr/share/tessdata",
|
||||
"Language": "eng"
|
||||
}
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user