protected override void CellAnnotation(AnnotationArgs args, AnnotationResult result)
{
if (args.FieldName == nameof(LoginUser.PasswordHash) || args.FieldName == nameof(LoginUser.PasswordSalt))
{
result.IsPassword = true;
}
}
public static void Check(string expression, AnnotationResult result)
{
Assert.Equal(0, result.DiagnosticResults.Count);
Assert.Equal(
expression,
string.Join("", result.TextChunks.Select(ch => ch.TextValue)));
}
protected override void CellAnnotation(AnnotationArgs args, AnnotationResult result)
{
if (args.FieldName == nameof(Feedback.AttachmentFileName))
{
result.IsFileUpload = true;
}
}
protected override void CellAnnotation(AnnotationArgs args, AnnotationResult result)
{
if (args.FieldName == nameof(Feedback.AttachmentFileName) && args.Row.AttachmentData != null)
{
result.Html = $"<a href='/feedback/{ args.Row.Name }'>{ args.Row.AttachmentFileName }</a>";
}
}
protected override void CellAnnotation(AnnotationArgs args, AnnotationResult result)
{
if (args.FieldName == nameof(StorageFileDisplay.FileName))
{
result.IsFileUpload = true;
if (args.Row.IsData != null)
{
result.HtmlRight = $"<a href=\"" + "/assets/" + args.Row.FileName + "\">" + "Open" + "</a>";
}
}
}
public static AnnotationResultSummary Create(AnnotationResult annotationResult, ErrorCategory?errorCategory, string errorMessage)
{
string fileName = Path.GetFileName(annotationResult?.filePath);
return(new AnnotationResultSummary
{
ErrorCategory = errorCategory,
ErrorMessage = errorMessage,
FileName = fileName
});
}
private static AnnotationResult HandleException(StringBuilder runLog, AnnotationResult result, Exception e, string snsTopicArn)
{
Logger.Log(e);
result.status = e.Message;
result.errorCategory = ExceptionUtilities.ExceptionToErrorCategory(e);
Logger.WriteLine($"Error Category: {result.errorCategory}");
if (result.errorCategory != ErrorCategory.UserError)
{
string snsMessage = SNS.CreateMessage(runLog.ToString(), result.status, e.StackTrace);
SNS.SendMessage(snsTopicArn, snsMessage);
}
LogUtilities.LogObject("Result", result);
return(result);
}
protected override void CellAnnotationFilterNew(AnnotationFilterNewArgs args, AnnotationResult result)
{
if (args.IsNew && args.FieldName == nameof(StorageFileDisplay.FileName))
{
result.IsFileUpload = true;
}
}
// ReSharper disable once UnusedMember.Global
public AnnotationResult Run(AnnotationConfig config, ILambdaContext context)
{
var result = new AnnotationResult {
id = config.id
};
string snsTopicArn = null;
var runLog = new StringBuilder();
try
{
LogUtilities.UpdateLogger(context.Logger, runLog);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
LambdaUtilities.DeleteTempOutput();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
string vcfUrl = config.vcfUrl;
using (var annotationResources = GetAnnotationResources(config))
{
if (annotationResources.InputStartVirtualPosition == -1)
{
return(GetSuccessOutput(result));
}
long fileOffset = VirtualPosition.From(annotationResources.InputStartVirtualPosition).FileOffset;
using (var preloadVcfStream = PersistentStreamUtils.GetReadStream(vcfUrl, fileOffset))
{
annotationResources.GetVariantPositions(new BlockGZipStream(preloadVcfStream, CompressionMode.Decompress), config.annotationRange.ToGenomicRange(annotationResources.SequenceProvider.RefNameToChromosome));
}
Logger.WriteLine("Scan for positions to preload complete.");
using (var aes = new AesCryptoServiceProvider())
{
FileMetadata jsonMetadata, jasixMetadata;
string jsonPath = Path.GetTempPath() + LambdaUrlHelper.JsonSuffix;
string jasixPath = jsonPath + LambdaUrlHelper.JsonIndexSuffix;
using (var inputVcfStream = new BlockGZipStream(PersistentStreamUtils.GetReadStream(vcfUrl, fileOffset), CompressionMode.Decompress))
using (var headerStream = config.annotationRange == null ? null : new BlockGZipStream(PersistentStreamUtils.GetReadStream(vcfUrl), CompressionMode.Decompress))
//
using (var jsonFileStream = FileUtilities.GetCreateStream(jsonPath))
using (var jsonCryptoStream = new CryptoStream(jsonFileStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var jsonMd5Stream = new MD5Stream(jsonCryptoStream))
//
using (var jasixFileStream = FileUtilities.GetCreateStream(jasixPath))
using (var jasixCryptoStream = new CryptoStream(jasixFileStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var jasixMd5Stream = new MD5Stream(jasixCryptoStream))
{
IVcfFilter vcfFilter = config.annotationRange == null
? new NullVcfFilter() as IVcfFilter
: new VcfFilter(config.annotationRange.ToGenomicRange(annotationResources.SequenceProvider.RefNameToChromosome));
using (var jsonCompressStream = new BlockGZipStream(jsonMd5Stream, CompressionMode.Compress))
{
StreamAnnotation.Annotate(headerStream, inputVcfStream, jsonCompressStream, jasixMd5Stream, annotationResources, vcfFilter, true);
}
Logger.WriteLine("Annotation done.");
jsonMetadata = jsonMd5Stream.GetFileMetadata();
jasixMetadata = jasixMd5Stream.GetFileMetadata();
}
result.filePath = S3Utilities.GetKey(config.outputDir.path, config.outputPrefix + LambdaUrlHelper.JsonSuffix);
string jasixKey = result.filePath + LambdaUrlHelper.JsonIndexSuffix;
var s3Client = config.outputDir.GetS3Client(context.RemainingTime);
s3Client.DecryptUpload(config.outputDir.bucketName, jasixKey, jasixPath, aes, jasixMetadata);
s3Client.DecryptUpload(config.outputDir.bucketName, result.filePath, jsonPath, aes, jsonMetadata);
Logger.WriteLine("Nirvana result files uploaded.");
}
}
LambdaUtilities.DeleteTempOutput();
if (string.IsNullOrEmpty(result.filePath))
{
throw new FileNotFoundException();
}
return(GetSuccessOutput(result));
}
catch (Exception exception)
{
LambdaUtilities.DeleteTempOutput();
return(HandleException(runLog, result, exception, snsTopicArn));
}
}
private static AnnotationResult GetSuccessOutput(AnnotationResult result)
{
result.status = LambdaUtilities.SuccessMessage;
LogUtilities.LogObject("Result", result);
return(result);
}
