// 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));
}
}
