private static ExitCodes ProgramExecution()
{
var omimSchema = OmimSchema.Get();
var omimParser = new OmimParser(_mimToGeneFile, _omimJsonFile, omimSchema);
var version = omimParser.GetVersion();
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.GeneFileSuffix)))
using (var ngaWriter = new NgaWriter(nsaStream, version, SaCommon.OmimTag, SaCommon.SchemaVersion, true))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.GeneFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
var omimItems = omimParser.GetItems();
var geneToItems = OmimUtilities.GetGeneToOmimEntriesAndSchema(omimItems);
ngaWriter.Write(geneToItems);
schemaWriter.Write(omimSchema);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
_apiKey = GetEnvironmentVariable(OmimApiKeyEnvironmentVariableName);
if (_apiKey == null)
{
throw new InvalidDataException("Please set the OMIM API key as the environment variable \"OmimApiKey\".");
}
var version = OmimVersion.GetVersion();
string outFileName = $"{version.Name}_{version.Version}";
string dumpFilePath = Path.Combine(_outputDirectory, OmimDumpFileBaseName + version.Version + OmimDumpFileSuffix);
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = OmimUtilities.ParseUniversalGeneArchive(_inputReferencePath, _universalGeneArchivePath);
var geneSymbolUpdater = new GeneSymbolUpdater(entrezGeneIdToSymbol, ensemblGeneIdToSymbol);
var omimSchema = OmimSchema.Get();
using (var omimParser = new OmimParser(geneSymbolUpdater, omimSchema, _apiKey, dumpFilePath))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(nsaStream, version, SaCommon.OmimTag, SaCommon.SchemaVersion, true))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
var omimItems = omimParser.GetItems();
var geneToItems = OmimUtilities.GetGeneToOmimEntriesAndSchema(omimItems);
ngaWriter.Write(geneToItems);
schemaWriter.Write(omimSchema);
}
geneSymbolUpdater.DisplayStatistics();
using (var writer = new StreamWriter(FileUtilities.GetCreateStream("UpdatedGeneSymbols.txt")))
{
geneSymbolUpdater.WriteUpdatedGeneSymbols(writer);
}
return(ExitCodes.Success);
}