public async Task ImportObservations(
[QueueTrigger(ImportsAvailableQueue)] ImportObservationsMessage message)
{
try
{
await _fileImportService.ImportObservations(message, DbUtils.CreateStatisticsDbContext());
}
catch (Exception e)
{
// If deadlock exception then throw & try up to 3 times
if (e is SqlException exception && exception.Number == 1205)
{
_logger.LogInformation($"{GetType().Name} : Handling known exception when processing Import: " +
$"{message.Id} : {exception.Message} : transaction will be retried");
throw;
}
var ex = GetInnerException(e);
_logger.LogError(ex, $"{GetType().Name} function FAILED for : Import: " +
$"{message.Id} : {ex.Message}");
await _dataImportService.FailImport(message.Id);
}
}
public async Task CheckComplete_SingleDataFileCompleted_AlreadyFinished()
{
await FinishedStatuses.ForEachAsync(async finishedStatus =>
{
var message = new ImportObservationsMessage
{
ReleaseId = Guid.NewGuid(),
NumBatches = 1,
DataFileName = "my_data_file.csv",
TotalRows = 2,
SubjectId = Guid.NewGuid()
};
var importStatusService = new Mock <IImportStatusService>(Strict);
var service = BuildFileImportService(
importStatusService: importStatusService.Object);
importStatusService
.Setup(s => s.GetImportStatus(message.ReleaseId, message.DataFileName))
.ReturnsAsync(new ImportStatus
{
Status = finishedStatus
});
var dbContext = StatisticsDbUtils.InMemoryStatisticsDbContext();
await using (dbContext)
{
await service.CheckComplete(message.ReleaseId, message, dbContext);
}
MockUtils.VerifyAllMocks(importStatusService);
});
}
public async Task ImportObservations(ImportObservationsMessage message, StatisticsDbContext context)
{
var import = await _dataImportService.GetImport(message.Id);
_logger.LogInformation($"Importing Observations for {import.File.Filename} batchNo {message.BatchNo}");
if (import.Status.IsFinished())
{
_logger.LogInformation($"Import for {import.File.Filename} already finished with state " +
$"{import.Status} - ignoring Observations in file {message.ObservationsFilePath}");
return;
}
if (import.Status == CANCELLING)
{
_logger.LogInformation($"Import for {import.File.Filename} is " +
$"{import.Status} - ignoring Observations in file {message.ObservationsFilePath} " +
"and marking import as CANCELLED");
await _dataImportService.UpdateStatus(message.Id, CANCELLED, 100);
return;
}
var subject = await context.Subject.FindAsync(import.SubjectId);
var datafileStream = await _blobStorageService.StreamBlob(PrivateReleaseFiles, message.ObservationsFilePath);
var dataFileTable = DataTableUtils.CreateFromStream(datafileStream);
var metaFileStream = await _blobStorageService.StreamBlob(PrivateReleaseFiles, import.MetaFile.Path());
var metaFileTable = DataTableUtils.CreateFromStream(metaFileStream);
await context.Database.CreateExecutionStrategy().Execute(async() =>
{
await using var transaction = await context.Database.BeginTransactionAsync();
await _importerService.ImportObservations(
import,
dataFileTable.Columns,
dataFileTable.Rows,
subject,
_importerService.GetMeta(metaFileTable, subject, context),
message.BatchNo,
context
);
await transaction.CommitAsync();
await context.Database.CloseConnectionAsync();
});
if (import.NumBatches > 1)
{
await _blobStorageService.DeleteBlob(PrivateReleaseFiles, message.ObservationsFilePath);
}
await CheckComplete(message, context);
}
public async Task CheckComplete_LastBatchFileCompleted_HasErrors()
{
var message = new ImportObservationsMessage
{
ReleaseId = Guid.NewGuid(),
NumBatches = 2,
DataFileName = "my_data_file.csv",
TotalRows = 2,
SubjectId = Guid.NewGuid()
};
var importStatusService = new Mock <IImportStatusService>(Strict);
var fileStorageService = new Mock <IFileStorageService>();
var service = BuildFileImportService(
importStatusService: importStatusService.Object,
fileStorageService: fileStorageService.Object);
importStatusService
.Setup(s => s.GetImportStatus(message.ReleaseId, message.DataFileName))
.ReturnsAsync(new ImportStatus
{
Status = STAGE_4,
Errors = "an error"
});
fileStorageService
.Setup(s => s.GetNumBatchesRemaining(message.ReleaseId, message.DataFileName))
.ReturnsAsync(0);
importStatusService
.Setup(s => s.UpdateStatus(
message.ReleaseId, message.DataFileName, FAILED, 100))
.Returns(Task.CompletedTask);
var dbContext = StatisticsDbUtils.InMemoryStatisticsDbContext();
await using (dbContext)
{
await dbContext.Observation.AddRangeAsync(
new Observation
{
SubjectId = message.SubjectId
},
new Observation
{
SubjectId = message.SubjectId
});
await dbContext.SaveChangesAsync();
await service.CheckComplete(message.ReleaseId, message, dbContext);
}
MockUtils.VerifyAllMocks(importStatusService, fileStorageService);
}
public async Task CheckComplete_SingleDataFileCompleted_HasIncorrectObservationCount()
{
var message = new ImportObservationsMessage
{
ReleaseId = Guid.NewGuid(),
NumBatches = 1,
DataFileName = "my_data_file.csv",
TotalRows = 3,
SubjectId = Guid.NewGuid()
};
var importStatusService = new Mock <IImportStatusService>(Strict);
var batchService = new Mock <IBatchService>(Strict);
var service = BuildFileImportService(
importStatusService: importStatusService.Object,
batchService: batchService.Object);
importStatusService
.Setup(s => s.GetImportStatus(message.ReleaseId, message.DataFileName))
.ReturnsAsync(new ImportStatus
{
Status = STAGE_4,
});
batchService
.Setup(s => s.FailImport(message.ReleaseId, message.DataFileName, new List <ValidationError>
{
new ValidationError(
$"Number of observations inserted (2) " +
$"does not equal that expected ({message.TotalRows}) : Please delete & retry"
)
}))
.Returns(Task.CompletedTask);
var dbContext = StatisticsDbUtils.InMemoryStatisticsDbContext();
await using (dbContext)
{
await dbContext.Observation.AddRangeAsync(
new Observation
{
SubjectId = message.SubjectId
},
new Observation
{
SubjectId = message.SubjectId
});
await dbContext.SaveChangesAsync();
await service.CheckComplete(message.ReleaseId, message, dbContext);
}
MockUtils.VerifyAllMocks(importStatusService, batchService);
}
public async Task CheckComplete(ImportObservationsMessage message, StatisticsDbContext context)
{
var import = await _dataImportService.GetImport(message.Id);
if (import.Status.IsFinished())
{
_logger.LogInformation($"Import for {import.File.Filename} is already finished in " +
$"state {import.Status} - not attempting to mark as completed or failed");
return;
}
if (import.Status.IsAborting())
{
_logger.LogInformation($"Import for {import.File.Filename} is trying to abort in " +
$"state {import.Status} - not attempting to mark as completed or failed, but " +
$"instead marking as {import.Status.GetFinishingStateOfAbortProcess()}, the final " +
$"state of the aborting process");
await _dataImportService.UpdateStatus(message.Id, import.Status.GetFinishingStateOfAbortProcess(), 100);
return;
}
if (import.NumBatches == 1 || await _batchService.GetNumBatchesRemaining(import.File) == 0)
{
var observationCount = context.Observation.Count(o => o.SubjectId.Equals(import.SubjectId));
if (!observationCount.Equals(import.TotalRows))
{
await _dataImportService.FailImport(message.Id,
$"Number of observations inserted ({observationCount}) " +
$"does not equal that expected ({import.TotalRows}) : Please delete & retry");
}
else
{
if (import.Errors.Count == 0)
{
await _dataImportService.UpdateStatus(message.Id, COMPLETE, 100);
}
else
{
await _dataImportService.UpdateStatus(message.Id, FAILED, 100);
}
}
}
else
{
var numBatchesRemaining = await _batchService.GetNumBatchesRemaining(import.File);
var percentageComplete = (double)(import.NumBatches - numBatchesRemaining) / import.NumBatches * 100;
await _dataImportService.UpdateStatus(message.Id, STAGE_4, percentageComplete);
}
}
public async Task CheckComplete_BatchedFilesStillProcessing()
{
var file = new File
{
Id = Guid.NewGuid(),
Filename = "my_data_file.csv"
};
var import = new DataImport
{
Id = Guid.NewGuid(),
Errors = new List <DataImportError>(),
FileId = file.Id,
File = file,
SubjectId = Guid.NewGuid(),
Status = STAGE_4,
NumBatches = 2,
TotalRows = 2
};
var batchService = new Mock <IBatchService>(Strict);
var dataImportService = new Mock <IDataImportService>(Strict);
batchService
.Setup(s => s.GetNumBatchesRemaining(import.File))
.ReturnsAsync(1);
dataImportService
.Setup(s => s.GetImport(import.Id))
.ReturnsAsync(import);
dataImportService
.Setup(s => s.UpdateStatus(
import.Id, STAGE_4, 50))
.Returns(Task.CompletedTask);
var statisticsDbContextId = Guid.NewGuid().ToString();
await using (var statisticsDbContext = InMemoryStatisticsDbContext(statisticsDbContextId))
{
var service = BuildFileImportService(batchService: batchService.Object,
dataImportService: dataImportService.Object);
var message = new ImportObservationsMessage
{
Id = import.Id
};
await service.CheckComplete(message, statisticsDbContext);
}
MockUtils.VerifyAllMocks(batchService, dataImportService);
}
public async Task CheckComplete_LastBatchFileCompleted_Aborting()
{
await AbortingStatuses
.ToAsyncEnumerable()
.ForEachAwaitAsync(async abortingStatus =>
{
var file = new File
{
Id = Guid.NewGuid(),
Filename = "my_data_file.csv"
};
var import = new DataImport
{
Id = Guid.NewGuid(),
Errors = new List <DataImportError>(),
FileId = file.Id,
File = file,
SubjectId = Guid.NewGuid(),
Status = abortingStatus,
NumBatches = 2,
TotalRows = 2
};
var dataImportService = new Mock <IDataImportService>(Strict);
dataImportService
.Setup(s => s.GetImport(import.Id))
.ReturnsAsync(import);
dataImportService
.Setup(s => s.UpdateStatus(
import.Id, abortingStatus.GetFinishingStateOfAbortProcess(), 100))
.Returns(Task.CompletedTask);
var statisticsDbContextId = Guid.NewGuid().ToString();
await using (var statisticsDbContext = InMemoryStatisticsDbContext(statisticsDbContextId))
{
var service = BuildFileImportService(dataImportService: dataImportService.Object);
var message = new ImportObservationsMessage
{
Id = import.Id
};
await service.CheckComplete(message, statisticsDbContext);
}
MockUtils.VerifyAllMocks(dataImportService);
});
}
public async Task CheckComplete_LastBatchFileCompleted_Aborting()
{
await AbortingStatuses.ForEachAsync(async abortingStatus =>
{
var message = new ImportObservationsMessage
{
ReleaseId = Guid.NewGuid(),
NumBatches = 2,
DataFileName = "my_data_file.csv",
TotalRows = 2,
SubjectId = Guid.NewGuid()
};
var importStatusService = new Mock <IImportStatusService>(Strict);
var fileStorageService = new Mock <IFileStorageService>();
var service = BuildFileImportService(
importStatusService: importStatusService.Object,
fileStorageService: fileStorageService.Object);
var currentStatus = new ImportStatus
{
Status = abortingStatus
};
importStatusService
.Setup(s => s.GetImportStatus(message.ReleaseId, message.DataFileName))
.ReturnsAsync(currentStatus);
importStatusService
.Setup(s => s.UpdateStatus(
message.ReleaseId, message.DataFileName, currentStatus.GetFinishingStateOfAbortProcess(), 100))
.Returns(Task.CompletedTask);
var dbContext = StatisticsDbUtils.InMemoryStatisticsDbContext();
await using (dbContext)
{
await service.CheckComplete(message.ReleaseId, message, dbContext);
}
MockUtils.VerifyAllMocks(importStatusService, fileStorageService);
});
}
public async Task CheckComplete_BatchedFilesStillProcessing()
{
var message = new ImportObservationsMessage
{
ReleaseId = Guid.NewGuid(),
NumBatches = 2,
DataFileName = "my_data_file.csv",
TotalRows = 2,
SubjectId = Guid.NewGuid(),
BatchNo = 1
};
var importStatusService = new Mock <IImportStatusService>(Strict);
var fileStorageService = new Mock <IFileStorageService>();
var service = BuildFileImportService(
importStatusService: importStatusService.Object,
fileStorageService: fileStorageService.Object);
importStatusService
.Setup(s => s.GetImportStatus(message.ReleaseId, message.DataFileName))
.ReturnsAsync(new ImportStatus
{
Status = STAGE_4
});
fileStorageService
.Setup(s => s.GetNumBatchesRemaining(message.ReleaseId, message.DataFileName))
.ReturnsAsync(1);
importStatusService
.Setup(s => s.UpdateStatus(
message.ReleaseId, message.DataFileName, STAGE_4, 50))
.Returns(Task.CompletedTask);
var dbContext = StatisticsDbUtils.InMemoryStatisticsDbContext();
await using (dbContext)
{
await service.CheckComplete(message.ReleaseId, message, dbContext);
}
MockUtils.VerifyAllMocks(importStatusService, fileStorageService);
}
public async Task CheckComplete_LastBatchFileCompleted_HasIncorrectObservationCount()
{
var file = new File
{
Id = Guid.NewGuid(),
Filename = "my_data_file.csv"
};
var import = new DataImport
{
Id = Guid.NewGuid(),
Errors = new List <DataImportError>(),
FileId = file.Id,
File = file,
SubjectId = Guid.NewGuid(),
Status = STAGE_4,
NumBatches = 2,
TotalRows = 3
};
var batchService = new Mock <IBatchService>(Strict);
var dataImportService = new Mock <IDataImportService>(Strict);
batchService
.Setup(s => s.GetNumBatchesRemaining(import.File))
.ReturnsAsync(0);
dataImportService
.Setup(s => s.GetImport(import.Id))
.ReturnsAsync(import);
dataImportService
.Setup(s => s.FailImport(import.Id,
$"Number of observations inserted (2) does not equal that expected ({import.TotalRows}) : Please delete & retry"))
.Returns(Task.CompletedTask);
var statisticsDbContextId = Guid.NewGuid().ToString();
await using (var statisticsDbContext = InMemoryStatisticsDbContext(statisticsDbContextId))
{
await statisticsDbContext.Observation.AddRangeAsync(
new Observation
{
SubjectId = import.SubjectId
},
new Observation
{
SubjectId = import.SubjectId
});
await statisticsDbContext.SaveChangesAsync();
}
await using (var statisticsDbContext = InMemoryStatisticsDbContext(statisticsDbContextId))
{
var service = BuildFileImportService(batchService: batchService.Object,
dataImportService: dataImportService.Object);
var message = new ImportObservationsMessage
{
Id = import.Id
};
await service.CheckComplete(message, statisticsDbContext);
}
MockUtils.VerifyAllMocks(batchService, dataImportService);
}
public async Task CheckComplete_LastBatchFileCompleted_HasErrors()
{
var file = new File
{
Id = Guid.NewGuid(),
Filename = "my_data_file.csv"
};
var import = new DataImport
{
Id = Guid.NewGuid(),
Errors = new List <DataImportError>
{
new DataImportError("an error")
},
FileId = file.Id,
File = file,
SubjectId = Guid.NewGuid(),
Status = STAGE_4,
NumBatches = 2,
TotalRows = 2
};
var batchService = new Mock <IBatchService>(Strict);
var dataImportService = new Mock <IDataImportService>(Strict);
batchService
.Setup(s => s.GetNumBatchesRemaining(import.File))
.ReturnsAsync(0);
dataImportService
.Setup(s => s.GetImport(import.Id))
.ReturnsAsync(import);
dataImportService
.Setup(s => s.UpdateStatus(
import.Id, FAILED, 100))
.Returns(Task.CompletedTask);
var statisticsDbContextId = Guid.NewGuid().ToString();
await using (var statisticsDbContext = InMemoryStatisticsDbContext(statisticsDbContextId))
{
await statisticsDbContext.Observation.AddRangeAsync(
new Observation
{
SubjectId = import.SubjectId
},
new Observation
{
SubjectId = import.SubjectId
});
await statisticsDbContext.SaveChangesAsync();
}
await using (var statisticsDbContext = InMemoryStatisticsDbContext(statisticsDbContextId))
{
var service = BuildFileImportService(batchService: batchService.Object,
dataImportService: dataImportService.Object);
var message = new ImportObservationsMessage
{
Id = import.Id
};
await service.CheckComplete(message, statisticsDbContext);
}
MockUtils.VerifyAllMocks(batchService, dataImportService);
}
public async Task ImportObservations(ImportObservationsMessage message, StatisticsDbContext context)
{
var releaseId = message.ReleaseId;
var status = await _importStatusService.GetImportStatus(releaseId, message.DataFileName);
if (status.IsFinished())
{
_logger.LogInformation($"Import for {message.DataFileName} already finished with state " +
$"{status.Status} - ignoring Observations in file {message.ObservationsFilePath}");
return;
}
if (status.Status == CANCELLING)
{
_logger.LogInformation($"Import for {message.DataFileName} is CANCELLING " +
$"{status.Status} - ignoring Observations in file {message.ObservationsFilePath} " +
$"and marking import as CANCELLED");
await _importStatusService.UpdateStatus(releaseId, message.DataFileName, CANCELLED, 100);
return;
}
var subjectData = await _fileStorageService.GetSubjectData(message.ReleaseId, message.ObservationsFilePath);
var releaseSubject = GetReleaseSubjectLink(message.ReleaseId, message.SubjectId, context);
await using var datafileStream = await _fileStorageService.StreamBlob(subjectData.DataBlob);
var dataFileTable = DataTableUtils.CreateFromStream(datafileStream);
await using var metaFileStream = await _fileStorageService.StreamBlob(subjectData.MetaBlob);
var metaFileTable = DataTableUtils.CreateFromStream(metaFileStream);
await context.Database.CreateExecutionStrategy().Execute(async() =>
{
await using var transaction = await context.Database.BeginTransactionAsync();
await _importerService.ImportObservations(
dataFileTable.Columns,
dataFileTable.Rows,
releaseSubject.Subject,
_importerService.GetMeta(metaFileTable, releaseSubject.Subject, context),
message.BatchNo,
message.RowsPerBatch,
context
);
await transaction.CommitAsync();
await context.Database.CloseConnectionAsync();
});
if (message.NumBatches > 1)
{
await _fileStorageService.DeleteBlobByPath(message.ObservationsFilePath);
}
await CheckComplete(releaseId, message, context);
}
public async Task CheckComplete(Guid releaseId, ImportObservationsMessage message, StatisticsDbContext context)
{
var import = await _importStatusService.GetImportStatus(releaseId, message.DataFileName);
if (import.IsFinished())
{
_logger.LogInformation($"Import for {message.DataFileName} is already finished in " +
$"state {import.Status} - not attempting to mark as completed or failed");
return;
}
if (import.IsAborting())
{
_logger.LogInformation($"Import for {message.DataFileName} is trying to abort in " +
$"state {import.Status} - not attempting to mark as completed or failed, but " +
$"instead marking as {import.GetFinishingStateOfAbortProcess()}, the final " +
$"state of the aborting process");
await _importStatusService.UpdateStatus(releaseId,
message.DataFileName,
import.GetFinishingStateOfAbortProcess(),
100);
return;
}
if (message.NumBatches == 1 ||
await _fileStorageService.GetNumBatchesRemaining(releaseId, message.DataFileName) == 0)
{
var observationCount = context.Observation.Count(o => o.SubjectId.Equals(message.SubjectId));
if (!observationCount.Equals(message.TotalRows))
{
await _batchService.FailImport(releaseId, message.DataFileName,
new List <ValidationError>
{
new ValidationError(
$"Number of observations inserted ({observationCount}) " +
$"does not equal that expected ({message.TotalRows}) : Please delete & retry"
)
}.AsEnumerable());
}
else
{
if (import.Errors.IsNullOrEmpty())
{
await _importStatusService.UpdateStatus(releaseId, message.DataFileName, COMPLETE, 100);
}
else
{
await _importStatusService.UpdateStatus(releaseId, message.DataFileName, FAILED, 100);
}
}
}
else
{
var numBatchesRemaining =
await _fileStorageService.GetNumBatchesRemaining(releaseId, message.DataFileName);
var percentageComplete = (double)(message.NumBatches - numBatchesRemaining) / message.NumBatches * 100;
await _importStatusService.UpdateStatus(releaseId,
message.DataFileName,
STAGE_4,
percentageComplete);
}
}
