Merge pull request #399 from Project-MONAI/release/0.3.21

Release/0.3.21

src/Api/Storage/FileStorageMetadata.cs

@@ -116,5 +116,7 @@ public virtual void SetFailed()
         {
             File.SetFailed();
         }
+
+        public string? PayloadId { get; set; }
     }
 }

src/Configuration/ConfigurationValidator.cs

@@ -120,7 +120,7 @@ private bool IsValidDirectory(string source, string directory)
         private bool IsValidBucketName(string source, string bucketName)
         {
             var valid = IsNotNullOrWhiteSpace(source, bucketName);
-            var regex = new Regex("(?=^.{3,63}$)(^[a-z0-9]+[a-z0-9\\-]+[a-z0-9]+$)");
+            var regex = new Regex("(?=^.{3,63}$)(^[a-z0-9]+[a-z0-9\\-]+[a-z0-9]+$)", new RegexOptions(), TimeSpan.FromSeconds(5));
             if (!regex.IsMatch(bucketName))
             {
                 valid = false;

src/Database/EntityFramework/Test/SourceApplicationEntityRepositoryTest.cs

@@ -119,6 +119,7 @@ public async Task GivenAAETitleName_WhenFindByAETAsyncIsCalled_ExpectItToReturnM
             Assert.Equal("AET1", actual.FirstOrDefault()!.Name);
 
             actual = await store.FindByAETAsync("AET6").ConfigureAwait(false);
+            Assert.NotNull(actual);
             Assert.Empty(actual);
         }
 

src/Database/MongoDB/Integration.Test/SourceApplicationEntityRepositoryTest.cs

@@ -124,6 +124,7 @@ public async Task GivenAETitle_WhenFindByAETitleAsyncIsCalled_ExpectItToReturnMa
             Assert.Equal("AET1", actual.FirstOrDefault()!.Name);
 
             actual = await store.FindByAETAsync("AET6").ConfigureAwait(false);
+            Assert.NotNull(actual);
             Assert.Empty(actual);
         }
 

src/InformaticsGateway/Logging/Log.4000.ObjectUploadService.cs

@@ -27,20 +27,20 @@ public static partial class Log
         [LoggerMessage(EventId = 4001, Level = LogLevel.Debug, Message = "Upload statistics: {threads} threads, {seconds} seconds.")]
         public static partial void UploadStats(this ILogger logger, int threads, double seconds);
 
-        [LoggerMessage(EventId = 4002, Level = LogLevel.Debug, Message = "Uploading file to temporary store at {filePath}.")]
-        public static partial void UploadingFileToTemporaryStore(this ILogger logger, string filePath);
+        [LoggerMessage(EventId = 4002, Level = LogLevel.Debug, Message = "Uploading file to storeage at {filePath}.")]
+        public static partial void UploadingFileToStoreage(this ILogger logger, string filePath);
 
         [LoggerMessage(EventId = 4003, Level = LogLevel.Information, Message = "Instance queued for upload {identifier}. Items in queue {count} using memory {memoryUsageKb}KB.")]
         public static partial void InstanceAddedToUploadQueue(this ILogger logger, string identifier, int count, double memoryUsageKb);
 
         [LoggerMessage(EventId = 4004, Level = LogLevel.Debug, Message = "Error removing objects that are pending upload during startup.")]
         public static partial void ErrorRemovingPendingUploadObjects(this ILogger logger, Exception ex);
 
-        [LoggerMessage(EventId = 4005, Level = LogLevel.Error, Message = "Error uploading temporary store. Waiting {timeSpan} before next retry. Retry attempt {retryCount}.")]
+        [LoggerMessage(EventId = 4005, Level = LogLevel.Error, Message = "Error uploading storeage. Waiting {timeSpan} before next retry. Retry attempt {retryCount}.")]
         public static partial void ErrorUploadingFileToTemporaryStore(this ILogger logger, TimeSpan timespan, int retryCount, Exception ex);
 
-        [LoggerMessage(EventId = 4006, Level = LogLevel.Information, Message = "File uploaded to temporary store at {filePath}.")]
-        public static partial void UploadedFileToTemporaryStore(this ILogger logger, string filePath);
+        [LoggerMessage(EventId = 4006, Level = LogLevel.Information, Message = "File uploaded to storeage at {filePath}.")]
+        public static partial void UploadedFileToStoreage(this ILogger logger, string filePath);
 
         [LoggerMessage(EventId = 4007, Level = LogLevel.Debug, Message = "Items in queue {count}.")]
         public static partial void InstanceInUploadQueue(this ILogger logger, int count);

src/InformaticsGateway/Services/Connectors/DataRetrievalService.cs

@@ -198,8 +198,11 @@ private async Task NotifyNewInstance(InferenceRequest inferenceRequest, Dictiona
                 {
                     retrievedFiles[key].SetWorkflows(inferenceRequest.Application.Id);
                 }
+                var FileMeta = retrievedFiles[key];
+
+                var payloadId = await _payloadAssembler.Queue(inferenceRequest.TransactionId, retrievedFiles[key]).ConfigureAwait(false);
+                retrievedFiles[key].PayloadId = payloadId.ToString();
                 _uploadQueue.Queue(retrievedFiles[key]);
-                await _payloadAssembler.Queue(inferenceRequest.TransactionId, retrievedFiles[key]).ConfigureAwait(false);
             }
         }
 

src/InformaticsGateway/Services/Connectors/IPayloadAssembler.cs

@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+using System;
 using System.Threading;
 using System.Threading.Tasks;
 using Monai.Deploy.InformaticsGateway.Api.Storage;
@@ -30,15 +31,15 @@ internal interface IPayloadAssembler
         /// </summary>
         /// <param name="bucket">The bucket group the file belongs to.</param>
         /// <param name="file">Path to the file to be added to the payload bucket.</param>
-        Task Queue(string bucket, FileStorageMetadata file);
+        Task<Guid> Queue(string bucket, FileStorageMetadata file);
 
         /// <summary>
         /// Queue a new file for the spcified payload bucket.
         /// </summary>
         /// <param name="bucket">The bucket group the file belongs to.</param>
         /// <param name="file">Path to the file to be added to the payload bucket.</param>
         /// <param name="timeout">Number of seconds to wait for additional files.</param>
-        Task Queue(string bucket, FileStorageMetadata file, uint timeout);
+        Task<Guid> Queue(string bucket, FileStorageMetadata file, uint timeout);
 
         /// <summary>
         /// Dequeue a payload from the queue for the message broker to notify subscribers.

src/InformaticsGateway/Services/Connectors/PayloadAssembler.cs

@@ -87,15 +87,15 @@ private async Task RemovePendingPayloads()
         /// </summary>
         /// <param name="bucket">Name of the bucket where the file would be added to</param>
         /// <param name="file">Instance to be queued</param>
-        public async Task Queue(string bucket, FileStorageMetadata file) => await Queue(bucket, file, DEFAULT_TIMEOUT).ConfigureAwait(false);
+        public async Task<Guid> Queue(string bucket, FileStorageMetadata file) => await Queue(bucket, file, DEFAULT_TIMEOUT).ConfigureAwait(false);
 
         /// <summary>
         /// Queues a new instance of <see cref="FileStorageMetadata"/>.
         /// </summary>
         /// <param name="bucket">Name of the bucket where the file would be added to</param>
         /// <param name="file">Instance to be queued</param>
         /// <param name="timeout">Number of seconds the bucket shall wait before sending the payload to be processed. Note: timeout cannot be modified once the bucket is created.</param>
-        public async Task Queue(string bucket, FileStorageMetadata file, uint timeout)
+        public async Task<Guid> Queue(string bucket, FileStorageMetadata file, uint timeout)
         {
             Guard.Against.Null(file);
 
@@ -106,6 +106,7 @@ public async Task Queue(string bucket, FileStorageMetadata file, uint timeout)
             var payload = await CreateOrGetPayload(bucket, file.CorrelationId, timeout).ConfigureAwait(false);
             payload.Add(file);
             _logger.FileAddedToBucket(payload.Key, payload.Count);
+            return payload.PayloadId;
         }
 
         /// <summary>

src/InformaticsGateway/Services/Connectors/PayloadMoveActionHandler.cs

@@ -77,7 +77,6 @@ public async Task MoveFilesAsync(Payload payload, ActionBlock<Payload> moveQueue
             var stopwatch = Stopwatch.StartNew();
             try
             {
-                await Move(payload, cancellationToken).ConfigureAwait(false);
                 await NotifyIfCompleted(payload, notificationQueue, cancellationToken).ConfigureAwait(false);
             }
             catch (Exception ex)
@@ -127,149 +126,6 @@ private async Task NotifyIfCompleted(Payload payload, ActionBlock<Payload> notif
             }
         }
 
-        private async Task Move(Payload payload, CancellationToken cancellationToken)
-        {
-            Guard.Against.Null(payload);
-
-            _logger.MovingFIlesInPayload(payload.PayloadId, _options.Value.Storage.StorageServiceBucketName);
-
-            var options = new ParallelOptions
-            {
-                CancellationToken = cancellationToken,
-                MaxDegreeOfParallelism = _options.Value.Storage.ConcurrentUploads
-            };
-
-            var exceptions = new List<Exception>();
-            await Parallel.ForEachAsync(payload.Files, options, async (file, cancellationToke) =>
-            {
-                try
-                {
-                    switch (file)
-                    {
-                        case DicomFileStorageMetadata dicom:
-                            if (!string.IsNullOrWhiteSpace(dicom.JsonFile.TemporaryPath))
-                            {
-                                await MoveFile(payload.PayloadId, dicom.Id, dicom.JsonFile, cancellationToken).ConfigureAwait(false);
-                            }
-                            break;
-                    }
-
-                    await MoveFile(payload.PayloadId, file.Id, file.File, cancellationToken).ConfigureAwait(false);
-                }
-                catch (Exception ex)
-                {
-                    exceptions.Add(ex);
-                }
-            }).ConfigureAwait(false);
-
-            if (exceptions.Any())
-            {
-                throw new AggregateException(exceptions);
-            }
-        }
-
-        private async Task MoveFile(Guid payloadId, string identity, StorageObjectMetadata file, CancellationToken cancellationToken)
-        {
-            Guard.Against.NullOrWhiteSpace(identity);
-            Guard.Against.Null(file);
-
-            if (file.IsMoveCompleted)
-            {
-                _logger.AlreadyMoved(payloadId, file.UploadPath);
-                return;
-            }
-
-            _logger.MovingFileToPayloadDirectory(payloadId, file.UploadPath);
-
-            try
-            {
-                await _storageService.CopyObjectAsync(
-                    file.TemporaryBucketName,
-                    file.GetTempStoragPath(_options.Value.Storage.RemoteTemporaryStoragePath),
-                    _options.Value.Storage.StorageServiceBucketName,
-                    file.GetPayloadPath(payloadId),
-                    cancellationToken).ConfigureAwait(false);
-
-                await VerifyFileExists(payloadId, file, cancellationToken).ConfigureAwait(false);
-            }
-            catch (StorageObjectNotFoundException ex) when (ex.Message.Contains("Not found", StringComparison.OrdinalIgnoreCase)) // TODO: StorageLib shall not throw any errors from MINIO
-            {
-                // when file cannot be found on the Storage Service, we assume file has been moved previously by verifying the file exists on destination.
-                _logger.FileMissingInPayload(payloadId, file.GetTempStoragPath(_options.Value.Storage.RemoteTemporaryStoragePath), ex);
-                await VerifyFileExists(payloadId, file, cancellationToken).ConfigureAwait(false);
-            }
-            catch (StorageConnectionException ex)
-            {
-                _logger.StorageServiceConnectionError(ex);
-                throw new PayloadNotifyException(PayloadNotifyException.FailureReason.ServiceUnavailable);
-            }
-            catch (Exception ex)
-            {
-                _logger.PayloadMoveException(ex);
-                await LogFilesInMinIo(file.TemporaryBucketName, cancellationToken).ConfigureAwait(false);
-                throw new FileMoveException(file.GetTempStoragPath(_options.Value.Storage.RemoteTemporaryStoragePath), file.UploadPath, ex);
-            }
-
-            try
-            {
-                _logger.DeletingFileFromTemporaryBbucket(file.TemporaryBucketName, identity, file.TemporaryPath);
-                await _storageService.RemoveObjectAsync(file.TemporaryBucketName, file.GetTempStoragPath(_options.Value.Storage.RemoteTemporaryStoragePath), cancellationToken).ConfigureAwait(false);
-            }
-            catch (Exception)
-            {
-                _logger.ErrorDeletingFileAfterMoveComplete(file.TemporaryBucketName, identity, file.TemporaryPath);
-            }
-            finally
-            {
-                file.SetMoved(_options.Value.Storage.StorageServiceBucketName);
-            }
-        }
-
-        private async Task VerifyFileExists(Guid payloadId, StorageObjectMetadata file, CancellationToken cancellationToken)
-        {
-            await Policy
-               .Handle<VerifyObjectsException>()
-               .WaitAndRetryAsync(
-                   _options.Value.Storage.Retries.RetryDelays,
-                   (exception, timeSpan, retryCount, context) =>
-                   {
-                       _logger.ErrorUploadingFileToTemporaryStore(timeSpan, retryCount, exception);
-                   })
-               .ExecuteAsync(async () =>
-               {
-                   var internalCancellationTokenSource = CancellationTokenSource.CreateLinkedTokenSource(cancellationToken);
-                   internalCancellationTokenSource.CancelAfter(_options.Value.Storage.StorageServiceListTimeout);
-                   var exists = await _storageService.VerifyObjectExistsAsync(_options.Value.Storage.StorageServiceBucketName, file.GetPayloadPath(payloadId), cancellationToken).ConfigureAwait(false);
-                   if (!exists)
-                   {
-                       _logger.FileMovedVerificationFailure(payloadId, file.UploadPath);
-                       throw new PayloadNotifyException(PayloadNotifyException.FailureReason.MoveFailure, false);
-                   }
-               })
-               .ConfigureAwait(false);
-        }
-
-        private async Task LogFilesInMinIo(string bucketName, CancellationToken cancellationToken)
-        {
-            try
-            {
-                var internalCancellationTokenSource = CancellationTokenSource.CreateLinkedTokenSource(cancellationToken);
-                internalCancellationTokenSource.CancelAfter(_options.Value.Storage.StorageServiceListTimeout);
-                var listingResults = await _storageService.ListObjectsAsync(bucketName, recursive: true, cancellationToken: internalCancellationTokenSource.Token).ConfigureAwait(false);
-                _logger.FilesFounddOnStorageService(bucketName, listingResults.Count);
-                var files = new List<string>();
-                foreach (var item in listingResults)
-                {
-                    files.Add(item.FilePath);
-                }
-                _logger.FileFounddOnStorageService(bucketName, string.Join(Environment.NewLine, files));
-            }
-            catch (Exception ex)
-            {
-                _logger.ErrorListingFilesOnStorageService(ex);
-            }
-        }
-
         private async Task<PayloadAction> UpdatePayloadState(Payload payload, Exception ex, CancellationToken cancellationToken = default)
         {
             Guard.Against.Null(payload);

src/InformaticsGateway/Services/DicomWeb/IStreamsWriter.cs

@@ -168,12 +168,14 @@ private async Task SaveInstance(Stream stream, string studyInstanceUid, string w
             {
                 dicomInfo.SetWorkflows(workflowName);
             }
+            // for DICOMweb, use correlation ID as the grouping key
+            var payloadId = await _payloadAssembler.Queue(correlationId, dicomInfo, _configuration.Value.DicomWeb.Timeout).ConfigureAwait(false);
+            dicomInfo.PayloadId = payloadId.ToString();
 
             await dicomInfo.SetDataStreams(dicomFile, dicomFile.ToJson(_configuration.Value.Dicom.WriteDicomJson, _configuration.Value.Dicom.ValidateDicomOnSerialization), _configuration.Value.Storage.TemporaryDataStorage, _fileSystem, _configuration.Value.Storage.LocalTemporaryStoragePath).ConfigureAwait(false);
             _uploadQueue.Queue(dicomInfo);
 
-            // for DICOMweb, use correlation ID as the grouping key
-            await _payloadAssembler.Queue(correlationId, dicomInfo, _configuration.Value.DicomWeb.Timeout).ConfigureAwait(false);
+
             _logger.QueuedStowInstance();
 
             AddSuccess(null, uids);

src/InformaticsGateway/Services/Fhir/FhirService.cs

@@ -87,8 +87,9 @@ public async Task<FhirStoreResult> StoreAsync(HttpRequest request, string correl
                 throw new FhirStoreException(correlationId, $"Provided resource is of type '{content.InternalResourceType}' but request targeted type '{resourceType}'.", IssueType.Invalid);
             }
 
+            var payloadId = await _payloadAssembler.Queue(correlationId, content.Metadata, Resources.PayloadAssemblerTimeout).ConfigureAwait(false);
+            content.Metadata.PayloadId = payloadId.ToString();
             _uploadQueue.Queue(content.Metadata);
-            await _payloadAssembler.Queue(correlationId, content.Metadata, Resources.PayloadAssemblerTimeout).ConfigureAwait(false);
             _logger.QueuedStowInstance();
 
             content.StatusCode = StatusCodes.Status201Created;

src/InformaticsGateway/Services/HealthLevel7/MllpService.cs

@@ -170,8 +170,9 @@ private async Task OnDisconnect(IMllpClient client, MllpClientResult result)
                 {
                     var hl7Fileetadata = new Hl7FileStorageMetadata(client.ClientId.ToString());
                     await hl7Fileetadata.SetDataStream(message.HL7Message, _configuration.Value.Storage.TemporaryDataStorage, _fileSystem, _configuration.Value.Storage.LocalTemporaryStoragePath).ConfigureAwait(false);
+                    var payloadId = await _payloadAssembler.Queue(client.ClientId.ToString(), hl7Fileetadata).ConfigureAwait(false);
+                    hl7Fileetadata.PayloadId = payloadId.ToString();
                     _uploadQueue.Queue(hl7Fileetadata);
-                    await _payloadAssembler.Queue(client.ClientId.ToString(), hl7Fileetadata).ConfigureAwait(false);
                 }
             }
             catch (Exception ex)

src/InformaticsGateway/Services/Scp/ApplicationEntityHandler.cs

@@ -113,12 +113,14 @@ public async Task HandleInstanceAsync(DicomCStoreRequest request, string calledA
             }
 
             await dicomInfo.SetDataStreams(request.File, request.File.ToJson(_dicomJsonOptions, _validateDicomValueOnJsonSerialization), _options.Value.Storage.TemporaryDataStorage, _fileSystem, _options.Value.Storage.LocalTemporaryStoragePath).ConfigureAwait(false);
-            _uploadQueue.Queue(dicomInfo);
 
             var dicomTag = FellowOakDicom.DicomTag.Parse(_configuration.Grouping);
             _logger.QueueInstanceUsingDicomTag(dicomTag);
             var key = request.Dataset.GetSingleValue<string>(dicomTag);
-            await _payloadAssembler.Queue(key, dicomInfo, _configuration.Timeout).ConfigureAwait(false);
+
+            var payloadid = await _payloadAssembler.Queue(key, dicomInfo, _configuration.Timeout).ConfigureAwait(false);
+            dicomInfo.PayloadId = payloadid.ToString();
+            _uploadQueue.Queue(dicomInfo);
         }
 
         private bool AcceptsSopClass(string sopClassUid)