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());
}
public static IGeneAnnotationProvider GetGeneAnnotationProvider(AnnotationFiles files) => files?.NsiFiles == null ? null : new GeneAnnotationProvider(PersistentStreamUtils.GetStreams(files.NgaFiles));