public static void run(XicParameters parameters)
{
var jsonString = File.ReadAllText(parameters.jsonFilePath, Encoding.UTF8);
var validationErrors = JSONParser.ValidateJson(jsonString);
if (!validationErrors.IsNullOrEmpty())
{
var validationMessage = new StringBuilder("JSON validation error(s):\n");
foreach (var validationError in validationErrors)
{
if (validationError.ToString().Contains("ExcludedSchemaValidates"))
{
validationMessage.Append(
"Use M/Z and tolerance, M/Z start and M/Z end or sequence and tolerance, not a combination (with optional RT start and/or end).\n");
}
validationMessage.Append(
$"element start line number: {validationError.LineNumber}\n{validationError.ToString()}");
}
throw new RawFileParserException(validationMessage.ToString());
}
var xicData = JSONParser.ParseJSON(jsonString);
foreach (string rawFile in parameters.rawFileList)
{
var dataInstance = new XicData(xicData);
XicReader.ReadXic(rawFile, parameters.base64, dataInstance);
if (parameters.stdout)
{
StdOutputXicData(dataInstance);
}
else
{
// if outputDirectory has been defined, put output there.
string directory;
if (parameters.outputDirectory != null)
{
directory = parameters.outputDirectory;
}
// otherwise put output files into the same directory as the raw file input
else
{
directory = Path.GetDirectoryName(rawFile);
}
var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException(),
Path.GetFileNameWithoutExtension(rawFile) + ".json");
OutputXicData(dataInstance, outputFileName);
}
}
}
public XicParameters(XicParameters copy)
{
help = copy.help;
rawFileList = new ArrayList();
foreach (string fileName in copy.rawFileList)
{
rawFileList.Add(fileName);
}
jsonFilePath = copy.jsonFilePath;
outputDirectory = copy.outputDirectory;
printJsonExample = copy.printJsonExample;
outputFileName = copy.outputFileName;
base64 = copy.base64;
stdout = copy.stdout;
}
