public void Validate_NullGenomeAssembly_ThrowException()
{
SingleConfig config = GetConfig();
config.genomeAssembly = null;
Assert.Throws <UserErrorException>(() => config.Validate());
}
public void Validate_NullVariant_ThrowException()
{
SingleConfig config = GetConfig();
config.variant = null;
Assert.Throws <UserErrorException>(() => config.Validate());
}
public void Validate_Success()
{
SingleConfig config = GetConfig();
Exception ex = Record.Exception(() => { config.Validate(); });
Assert.Null(ex);
}
// ReSharper disable once UnusedMember.Global
public Stream Run(SingleConfig config, ILambdaContext context)
{
string snsTopicArn = null;
Stream response;
try
{
LogUtilities.UpdateLogger(context.Logger, null);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
config.Validate();
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(config.genomeAssembly);
var cacheConfiguration = new CacheConfiguration(genomeAssembly, config.supplementaryAnnotations, config.vepVersion);
bool preloadRequired = !string.IsNullOrEmpty(config.supplementaryAnnotations);
AnnotationResources annotationResources = GetAndCacheAnnotationResources(config, cacheConfiguration);
if (genomeAssembly != GenomeAssembly.hg19)
{
annotationResources.Annotator.EnableMitochondrialAnnotation();
}
(IPosition position, string[] sampleNames) = config.GetPositionAndSampleNames(annotationResources.SequenceProvider, annotationResources.RefMinorProvider);
if (position.Chromosome.IsEmpty())
{
throw new UserErrorException($"An unknown chromosome was specified ({config.variant.chromosome})");
}
string annotationResult = GetPositionAnnotation(position, annotationResources, sampleNames, preloadRequired);
response = SingleResult.Create(config.id, LambdaUrlHelper.SuccessMessage, annotationResult);
}
catch (Exception exception)
{
response = ExceptionHandler.GetStream(config.id, snsTopicArn, exception);
}
return(response);
}
