public static string GetGeneAnnotation(GeneConfig input, string saManifestFilePath, string saPathPrefix)
{
var geneAnnotationProvider = new GeneAnnotationProvider(PersistentStreamUtils.GetStreams(
GetNgaFileList(saManifestFilePath, saPathPrefix, input.ngaUrls).ToList()));
var sb = new StringBuilder(1024 * 1024);
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue(JasixCommons.HeaderSectionTag, GetHeader(geneAnnotationProvider), false);
//not all gene symbols have annotations. So, we need to check and only output the ones that are not null
var geneAnnotations = input.geneSymbols.Select(geneSymbol => geneAnnotationProvider.Annotate(geneSymbol))
.Where(annotation => !string.IsNullOrEmpty(annotation))
.ToList();
jsonObject.AddStringValues("genes", geneAnnotations, false);
sb.Append(JsonObject.CloseBrace);
// AWS lambda response message can not be larger than 6MB
if (sb.Length > 6_000_000)
{
throw new UserErrorException("Too many genes provided in the request. Please decrease the number of genes and try again later.");
}
return(sb.ToString());
}
// ReSharper disable once UnusedMember.Global
public Stream Run(GeneConfig config, ILambdaContext context)
{
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();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
config.Validate();
string result = GetGeneAnnotation(config, _saManifestUrl, _saPathPrefix);
return(LambdaResponse.Create(config.id, LambdaUrlHelper.SuccessMessage, result));
}
catch (Exception e)
{
return(HandleException(config.id, snsTopicArn, e));
}
}
public void Validate_NoId_ThrowException()
{
var input = new GeneConfig {
geneSymbols = new[] { "TP53" }
};
Assert.Throws <UserErrorException>(() => input.Validate());
}
public void Validate_EmptyGeneSymbols_ThrowException()
{
var input = new GeneConfig {
id = "test", geneSymbols = new string[] {}
};
Assert.Throws <UserErrorException>(() => input.Validate());
}
public void Validate_NoGeneSymbols_ThrowException()
{
var input = new GeneConfig {
id = "test"
};
Assert.Throws <UserErrorException>(() => input.Validate());
}
public void GetGeneAnnotation_AsExpected()
{
var input = new GeneConfig
{
id = "test",
geneSymbols = new[] { "TP53", "ZIC2", "LOC645752" },
ngaUrls = new[] { _customNgaPath }
};
string responseString = global::GeneAnnotationLambda.GeneAnnotationLambda.GetGeneAnnotation(input, _manifestPath, _prefix);
Assert.Contains("header", responseString);
Assert.Contains("TP53", responseString);
Assert.Contains("ZIC2", responseString);
Assert.Contains("clingenDosageSensitivityMap", responseString);
Assert.Contains("gnomAD", responseString);
Assert.Contains("omim", responseString);
Assert.Contains("InternalGeneAnnotation", responseString);
Assert.DoesNotContain("LOC645752", responseString);
}
