public static CustomResult GetSuccessResult(CustomConfig customSaConfig, CustomResult result, List <string> outputFiles)
{
Logger.WriteLine("All files uploaded.");
result.created = new FileList
{
bucketName = customSaConfig.outputDir.bucketName,
outputDir = customSaConfig.outputDir.path,
files = outputFiles.ToArray()
};
result.status = LambdaUtilities.SuccessMessage;
LogUtilities.LogObject("Result", result);
LambdaUtilities.DeleteTempOutput();
return(result);
}
private static CustomResult HandleException(StringBuilder runLog, CustomResult result, Exception e, string snsTopicArn)
{
Logger.Log(e);
var errorCategory = ExceptionUtilities.ExceptionToErrorCategory(e);
result.status = $"{errorCategory}: {e.Message}";
if (errorCategory != ErrorCategory.UserError)
{
string snsMessage = SNS.CreateMessage(runLog.ToString(), result.status, e.StackTrace);
SNS.SendMessage(snsTopicArn, snsMessage);
}
LogUtilities.LogObject("Result", result);
LambdaUtilities.DeleteTempOutput();
return(result);
}
// ReSharper disable once UnusedMember.Global
public CustomResult Run(CustomConfig config, ILambdaContext context)
{
var result = new CustomResult {
id = config.id
};
string snsTopicArn = null;
var runLog = new StringBuilder();
try
{
LogUtilities.UpdateLogger(context.Logger, runLog);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
LambdaUtilities.DeleteTempOutput();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
config.CheckRequiredFieldsNotNull();
var s3Client = config.outputDir.GetS3Client(context.RemainingTime);
config.CheckResourcesExist();
LambdaUtilities.DeleteTempOutput();
string inputFileName = config.tsvUrl.TrimEndFromFirst("?").TrimStartToLast("/");
Logger.WriteLine($"input file name is: {inputFileName}");
return(IsGeneAnnotationTsv(config.tsvUrl)
? GeneAnnotationCreator.Create(config, inputFileName, result, s3Client)
: VariantAnnotationCreator.Create(config, inputFileName, result, s3Client));
}
catch (Exception e)
{
return(HandleException(runLog, result, e, snsTopicArn));
}
}
// 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));
}
}
public static CustomResult Create(CustomConfig config, string inputFileName, CustomResult result, IS3Client s3Client)
{
string tempPath = Path.GetTempPath();
string inputBaseName = inputFileName.TrimEndFromFirst(".tsv");
string nsaFileName = inputBaseName + SaCommon.SaFileSuffix;
string localNsaPath = Path.Combine(tempPath, nsaFileName);
string localIndexPath = localNsaPath + SaCommon.IndexSufix;
string localSchemaPath = localNsaPath + SaCommon.JsonSchemaSuffix;
var outputFiles = new List <string>();
using (var aes = new AesCryptoServiceProvider())
{
FileMetadata nsaMetadata, indexMetadata, schemaMetadata;
List <CustomInterval> intervals;
string jsonTag;
SaJsonSchema intervalJsonSchema;
DataSourceVersion version;
GenomeAssembly genomeAssembly;
int nsaItemsCount;
ReportFor reportFor;
using (var customTsvStream = (PersistentStream)PersistentStreamUtils.GetReadStream(config.tsvUrl))
using (var parser = GetVariantAnnotationsParserFromCustomTsvStream(customTsvStream))
//
using (var nsaStream = FileUtilities.GetCreateStream(localNsaPath))
using (var nsaCryptoStream = new CryptoStream(nsaStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var nsaMd5Stream = new MD5Stream(nsaCryptoStream))
//
using (var indexStream = FileUtilities.GetCreateStream(localIndexPath))
using (var indexCryptoStream = new CryptoStream(indexStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var indexMd5Stream = new MD5Stream(indexCryptoStream))
//
using (var schemaStream = FileUtilities.GetCreateStream(localSchemaPath))
using (var schemaCryptoStream = new CryptoStream(schemaStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var schemaMd5Stream = new MD5Stream(schemaCryptoStream))
{
genomeAssembly = parser.Assembly;
result.genomeAssembly = genomeAssembly.ToString();
reportFor = parser.ReportFor;
using (var nsaWriter = CaUtilities.GetNsaWriter(nsaMd5Stream, indexMd5Stream, parser, inputFileName, parser.SequenceProvider, out version))
using (var schemaWriter = new StreamWriter(schemaMd5Stream))
{
(jsonTag, nsaItemsCount, intervalJsonSchema, intervals) = CaUtilities.WriteSmallVariants(parser, nsaWriter, schemaWriter);
}
nsaMetadata = nsaMd5Stream.GetFileMetadata();
indexMetadata = indexMd5Stream.GetFileMetadata();
schemaMetadata = schemaMd5Stream.GetFileMetadata();
}
if (nsaItemsCount > 0)
{
string nsaS3Path = string.Join('/', config.outputDir.path.Trim('/'), nsaFileName);
string indexS3Path = nsaS3Path + SaCommon.IndexSufix;
string schemaS3Path = nsaS3Path + SaCommon.JsonSchemaSuffix;
s3Client.DecryptUpload(config.outputDir.bucketName, nsaS3Path, localNsaPath, aes, nsaMetadata);
s3Client.DecryptUpload(config.outputDir.bucketName, indexS3Path, localIndexPath, aes,
indexMetadata);
s3Client.DecryptUpload(config.outputDir.bucketName, schemaS3Path, localSchemaPath, aes,
schemaMetadata);
outputFiles.Add(nsaFileName);
outputFiles.Add(nsaFileName + SaCommon.IndexSufix);
outputFiles.Add(nsaFileName + SaCommon.JsonSchemaSuffix);
}
if (intervals == null)
{
return(CustomAnnotationLambda.GetSuccessResult(config, result, outputFiles));
}
FileMetadata nsiMetadata, nsiSchemaMetadata;
string nsiFileName = inputBaseName + SaCommon.SiFileSuffix;
string localNsiPath = Path.Combine(tempPath, nsiFileName);
string localNsiSchemaPath = localNsiPath + SaCommon.JsonSchemaSuffix;
//
using (var nsiStream = FileUtilities.GetCreateStream(localNsiPath))
using (var nsiCryptoStream = new CryptoStream(nsiStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var nsiMd5Stream = new MD5Stream(nsiCryptoStream))
//
using (var nsiSchemaSteam = FileUtilities.GetCreateStream(localNsiSchemaPath))
using (var nsiSchemaCryptoStream =
new CryptoStream(nsiSchemaSteam, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var nsiSchemaMd5Stream = new MD5Stream(nsiSchemaCryptoStream))
{
using (var nsiWriter = CaUtilities.GetNsiWriter(nsiMd5Stream, version, genomeAssembly, jsonTag, reportFor))
using (var schemaWriter = new StreamWriter(nsiSchemaMd5Stream))
{
nsiWriter.Write(intervals);
schemaWriter.Write(intervalJsonSchema);
}
nsiMetadata = nsiMd5Stream.GetFileMetadata();
nsiSchemaMetadata = nsiSchemaMd5Stream.GetFileMetadata();
}
string nsiS3Path = string.Join('/', config.outputDir.path.Trim('/'), nsiFileName);
string nsiSchemaS3PathFile = nsiS3Path + SaCommon.JsonSchemaSuffix;
s3Client.DecryptUpload(config.outputDir.bucketName, nsiS3Path, localNsiPath, aes, nsiMetadata);
s3Client.DecryptUpload(config.outputDir.bucketName, nsiSchemaS3PathFile, localNsiSchemaPath, aes,
nsiSchemaMetadata);
outputFiles.Add(nsiFileName);
outputFiles.Add(nsiFileName + SaCommon.JsonSchemaSuffix);
}
LambdaUtilities.DeleteTempOutput();
return(CustomAnnotationLambda.GetSuccessResult(config, result, outputFiles));
}
public static CustomResult Create(CustomConfig config, string inputBaseName, CustomResult result, IS3Client s3Client)
{
string ngaFileName = inputBaseName + SaCommon.NgaFileSuffix;
string localNgaPath = Path.Combine(Path.GetTempPath(), ngaFileName);
string localSchemaPath = localNgaPath + SaCommon.JsonSchemaSuffix;
string localLogPath = Path.Combine(Path.GetTempPath(), LogFileName);
HttpUtilities.ValidateUrl(LambdaUrlHelper.GetUgaUrl());
var outputFiles = new List <string>();
using (var aes = new AesCryptoServiceProvider())
{
FileMetadata ngaMetadata, schemaMetadata, logMetaData;
using (var logStream = FileUtilities.GetCreateStream(localLogPath))
using (var logCryptoStream = new CryptoStream(logStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var logMd5Stream = new MD5Stream(logCryptoStream))
//
using (var customTsvStream = (PersistentStream)PersistentStreamUtils.GetReadStream(config.tsvUrl))
using (var parser = GetGeneAnnotationsParserFromCustomTsvStream(customTsvStream))
//
using (var ngaStream = FileUtilities.GetCreateStream(localNgaPath))
using (var ngaCryptoStream = new CryptoStream(ngaStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var ngaMd5Stream = new MD5Stream(ngaCryptoStream))
//
using (var schemaStream = FileUtilities.GetCreateStream(localSchemaPath))
using (var schemaCryptoStream = new CryptoStream(schemaStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var schemaMd5Stream = new MD5Stream(schemaCryptoStream))
{
using (var ngaWriter = CaUtilities.GetNgaWriter(ngaMd5Stream, parser, config.tsvUrl))
using (var schemaWriter = new StreamWriter(schemaMd5Stream))
using (var logWriter = new StreamWriter(logMd5Stream))
{
ngaWriter.Write(parser.GetItems(config.skipGeneIdValidation, logWriter));
schemaWriter.Write(parser.JsonSchema);
}
//all the writers have to be disposed before GetFileMetaData is called
ngaMetadata = ngaMd5Stream.GetFileMetadata();
schemaMetadata = schemaMd5Stream.GetFileMetadata();
logMetaData = logMd5Stream.GetFileMetadata();
}
if (config.skipGeneIdValidation)
{
string logS3Key = string.Join('/', config.outputDir.path.Trim('/'), LogFileName);
Logger.WriteLine("uploading log file to " + logS3Key);
s3Client.DecryptUpload(config.outputDir.bucketName, logS3Key, localLogPath, aes, logMetaData);
}
string nsaS3Path = string.Join('/', config.outputDir.path.Trim('/'), ngaFileName);
string schemaS3Path = nsaS3Path + SaCommon.JsonSchemaSuffix;
s3Client.DecryptUpload(config.outputDir.bucketName, nsaS3Path, localNgaPath, aes, ngaMetadata);
s3Client.DecryptUpload(config.outputDir.bucketName, schemaS3Path, localSchemaPath, aes, schemaMetadata);
outputFiles.Add(ngaFileName);
outputFiles.Add(ngaFileName + SaCommon.JsonSchemaSuffix);
LambdaUtilities.DeleteTempOutput();
return(CustomAnnotationLambda.GetSuccessResult(config, result, outputFiles));
}
}
