private static ExitCodes ProgramExecution()
{
(string hostName, string remoteCacheDir, string remoteReferencesDir, string manifestGRCh37,
string manifestGRCh38) = Configuration.Load();
List <GenomeAssembly> genomeAssemblies = GenomeAssemblyHelper.GetGenomeAssemblies(_genomeAssembly);
var client = new Client(hostName);
Console.Write("- downloading manifest... ");
Dictionary <GenomeAssembly, List <string> > remotePathsByGenomeAssembly =
Manifest.GetRemotePaths(client, genomeAssemblies, manifestGRCh37, manifestGRCh38);
(string cacheDir, string referencesDir, string saDir, List <string> outputDirectories) =
OutputDirectory.Create(_outputDirectory, genomeAssemblies);
var fileList = new List <RemoteFile>();
fileList.AddCacheFiles(genomeAssemblies, remoteCacheDir, cacheDir)
.AddReferenceFiles(genomeAssemblies, remoteReferencesDir, referencesDir)
.AddSupplementaryAnnotationFiles(remotePathsByGenomeAssembly, saDir);
Console.WriteLine($"{fileList.Count} files.\n");
// get rid of extra files in the output directories
OutputDirectory.Cleanup(fileList, outputDirectories);
// get length, checksum, and checks existence
Console.WriteLine("- downloading file metadata:");
AnnotationRepository.DownloadMetadata(client, fileList);
// remove obsolete files from the output directory
OutputDirectory.RemoveOldFiles(fileList);
// remove skipped files from our list
List <RemoteFile> filesToDownload = OutputDirectory.RemoveSkippedFiles(fileList);
// download the latest files
if (filesToDownload.Count > 0)
{
long numBytesToDownload = OutputDirectory.GetNumDownloadBytes(filesToDownload);
Console.WriteLine($"- downloading files ({MemoryUtilities.ToHumanReadable(numBytesToDownload)}):");
AnnotationRepository.DownloadFiles(client, filesToDownload);
}
// sanity check
OutputDirectory.CheckFiles(fileList);
bool foundError = fileList.Any(x => !x.Pass);
return(foundError ? ExitCodes.InvalidData : ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
(string hostName, string remoteCacheDir, string remoteReferencesDir, string manifestGRCh37,
string manifestGRCh38) = Configuration.Load();
List <GenomeAssembly> genomeAssemblies = GenomeAssemblyHelper.GetGenomeAssemblies(_genomeAssembly);
var client = new Client(hostName);
Dictionary <GenomeAssembly, List <string> > remotePathsByGenomeAssembly =
Manifest.GetRemotePaths(client, genomeAssemblies, manifestGRCh37, manifestGRCh38);
(string cacheDir, string referencesDir, string saDir) =
OutputDirectory.Create(_outputDirectory, genomeAssemblies);
var fileList = new List <RemoteFile>();
fileList.AddCacheFiles(genomeAssemblies, remoteCacheDir, cacheDir)
.AddReferenceFiles(genomeAssemblies, remoteReferencesDir, referencesDir)
.AddSupplementaryAnnotationFiles(remotePathsByGenomeAssembly, saDir)
.Download(client);
return(ExitCodes.Success);
}
