/// <summary>
/// Helper function to get the MethodXMLContext
/// </summary>
/// <param name="model">The instrument model</param>
/// <param name="version">The instrument version</param>
/// <returns></returns>
public static IMethodXMLContext CreateContext(string model = "", string version = "")
{
if (string.IsNullOrEmpty(model))
{
model = MethodXMLFactory.GetInstalledServerModel();
}
if (string.IsNullOrEmpty(version))
{
version = MethodXMLFactory.GetLatestInstalledVersion(model);
}
if (!MethodXMLFactory.GetInstalledInstrumentModels().Contains(model))
{
throw new ArgumentException("Cannot create method context for non-installed instrument model: " + model);
}
return(MethodXMLFactory.CreateContext(model, version));
}
/// <summary>
/// Prints information about the executing computer's TNG status
/// </summary>
public static IEnumerable <string> PrintInformation()
{
// Get all installed instruments for executing computer
// Searches the registry for installed TNG instruments.
// HKEY_LOCAL_MACHINE\SOFTWARE\Thermo Instruments\TNG
// or
// HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Thermo Instruments\TNG
var instruments = MethodXMLFactory.GetInstalledInstrumentModels();
yield return("== Configured Instruments ==");
int i = 1;
foreach (string instrument in instruments)
{
Console.WriteLine("{0,2}: {1}", i++, instrument);
// Get all installed instrument versions for this particular instrument (i.e., Fusion 1.1, 1.2, etc...)
var versions = MethodXMLFactory.GetInstalledVersions(instrument);
// TNG can be installed as Full (connected to instrument) or Workstation (just MethodEditor) mode.
var fullInstalledVersions = new HashSet <string>(MethodXMLFactory.GetFullInstalledVersions(instrument));
// The most recently installed version for this instrument model
var lastInstalledVersion = MethodXMLFactory.GetLatestInstalledVersion(instrument);
foreach (string version in versions)
{
yield return(string.Format("{0,8} ({1}){2}",
version,
fullInstalledVersions.Contains(version) ? "Full" : "WorkStation",
version == lastInstalledVersion ? " Latest Installed" : ""));
}
}
yield return("============================");
yield return(string.Format("Installed Server Model: {0}", MethodXMLFactory.GetInstalledServerModel()));
yield return(string.Format("Installed Server Version: {0}", MethodXMLFactory.GetInstalledServerVersion()));
}
/// <summary>
/// Applies the modification XML file to the method template, to produce a modified method file
/// </summary>
/// <param name="methodTemplate">The method to base off of</param>
/// <param name="methodModXML">The modifications to be applied to the template method</param>
/// <param name="outputMethod">The file path for the generated method</param>
/// <param name="model">The instrument model</param>
/// <param name="version">The instrument version</param>
/// <param name="enableValidation">Enable automatic validation on saving</param>
public static void ModifyMethod(string methodTemplate, string methodModXML, string outputMethod = "", string model = "", string version = "", bool enableValidation = true)
{
if (string.IsNullOrEmpty(methodTemplate))
{
throw new ArgumentException("A method file path must be specified", "Method Template");
}
if (string.IsNullOrEmpty(methodModXML))
{
throw new ArgumentException("A method modification path must be specified", "Method Modification");
}
// Handle relative/absolute paths
methodTemplate = Path.GetFullPath(methodTemplate);
methodModXML = Path.GetFullPath(methodModXML);
// These files are required
if (!File.Exists(methodTemplate))
{
throw new IOException("File Not Found: " + methodTemplate);
}
if (!File.Exists(methodModXML))
{
throw new IOException("File Not Found: " + methodModXML);
}
// Create output file path if not specified
if (string.IsNullOrEmpty(outputMethod))
{
outputMethod = methodTemplate.Replace(".meth", "_modified.meth");
}
outputMethod = Path.GetFullPath(outputMethod);
// Create output directory if doesn't exist
if (!Directory.Exists(Path.GetDirectoryName(outputMethod)))
{
Directory.CreateDirectory(Path.GetDirectoryName(outputMethod));
}
// If the instrument model is not specified, get the default installed one. (might not be the best)
if (string.IsNullOrEmpty(model))
{
model = MethodXMLFactory.GetInstalledServerModel();
if (string.IsNullOrEmpty(model))
{
var instruments = MethodXMLFactory.GetInstalledInstrumentModels();
if (instruments.Count > 1)
{
throw new Exception(string.Format("Unable to find default installed instrument, you have {0} instruments registered", instruments.Count));
}
else if (instruments.Count == 0)
{
throw new Exception("Unable to find any installed instruments!");
}
else
{
model = instruments[0];
}
}
}
// Get the type of instrument based on its name
InstrumentFamily instrumentFamily = GetInstrumentFamilyFromModel(model);
// Get the type of instrument modification based on the xml file
InstrumentFamily xmlInstrumentFamily = GetInstrumentFamilyFromXml(methodModXML);
// These two need to be equivalent to correctly apply the modifications
if (instrumentFamily != xmlInstrumentFamily)
{
throw new ArgumentException(string.Format("The specified xml ({0}) is not compatible with the instrument model ({1}, {2})", xmlInstrumentFamily, instrumentFamily, model));
}
using (IMethodXMLContext mxc = CreateContext(model, version))
using (IMethodXML xmlMeth = mxc.Create())
{
// Open the template method
xmlMeth.Open(methodTemplate);
// Set the validation flag
xmlMeth.EnableValidation(enableValidation);
// Call the correct modification method based on the instrument type
switch (instrumentFamily)
{
case InstrumentFamily.OrbitrapFusion:
xmlMeth.ApplyMethodModificationsFromXMLFile(methodModXML);
break;
case InstrumentFamily.TSQ:
xmlMeth.ImportMassListFromXMLFile(methodModXML);
break;
default:
throw new ArgumentException("Unsupported instrument model:" + model);
}
// Save the in memory method to the output file
xmlMeth.SaveAs(outputMethod);
}
}
