/// <summary>
/// Creates a .meth file from .xml
/// </summary>
/// <param name="xmlFilePath">The xml file path to create the method from</param>
/// <param name="outputMethod">The file path of the to be created method</param>
/// <param name="model">The instrument model (only TSQ)</param>
/// <param name="version">The instrument version</param>
public static void CreateMethod(string xmlFilePath, string outputMethod = "", string model = "", string version = "")
{
// Handle relative/absolute paths
xmlFilePath = Path.GetFullPath(xmlFilePath);
if (string.IsNullOrEmpty(outputMethod))
{
outputMethod = Path.ChangeExtension(xmlFilePath, ".meth");
}
outputMethod = Path.GetFullPath(outputMethod);
// Get the type of instrument based on its name
InstrumentFamily instrumentFamily = GetInstrumentFamilyFromModel(model);
if (instrumentFamily != InstrumentFamily.TSQ)
{
throw new ArgumentException("You can only create methods from TSQ xml files");
}
using (IMethodXMLContext mxc = CreateContext(model, version))
using (IMethodXML xmlMeth = mxc.Create())
{
// Loads the method from the xml
xmlMeth.LoadMethodFromXMLFile(xmlFilePath);
// Save the in memory method to the output file
xmlMeth.SaveAs(outputMethod);
}
}
public static void ExportMethod(string methodFile, string outputFile, string instrumentModel, string version)
{
methodFile = Path.GetFullPath(methodFile);
if (string.IsNullOrEmpty(outputFile))
{
outputFile = Path.ChangeExtension(methodFile, ".xml");
}
outputFile = Path.GetFullPath(outputFile);
// Get the type of instrument based on its name
InstrumentFamily instrumentFamily = GetInstrumentFamilyFromModel(instrumentModel);
if (instrumentFamily != InstrumentFamily.OrbitrapFusion)
{
throw new ArgumentException("You can only export Fusion/Tribrid method files");
}
string xml = "";
using (IMethodXMLContext mxc = CreateContext(instrumentModel, version))
using (IMethodXML xmlMeth = mxc.Create())
using (StreamWriter writer = new StreamWriter(outputFile))
{
xmlMeth.Open(methodFile);
xml = xmlMeth.ExportMethodToXML();
writer.Write(xml);
}
}
public void Build()
{
foreach (var methodTranList in MethodTrans)
{
Console.Error.WriteLine("MESSAGE: Exporting method {0}", Path.GetFileName(methodTranList.FinalMethod));
if (string.IsNullOrEmpty(methodTranList.TransitionList))
{
throw new IOException(string.Format("Failure creating method file {0}. The mass list is empty.", methodTranList.FinalMethod));
}
string outMeth = EnsureExtension(methodTranList.OutputMethod, ".meth"); // Thermo needs the extension to be .meth
if (!Equals(outMeth, methodTranList.OutputMethod) && File.Exists(methodTranList.OutputMethod))
{
File.Move(methodTranList.OutputMethod, outMeth);
}
try
{
using (IMethodXMLContext mxc = MethodXMLFactory.CreateContext(InstrumentType, InstrumentVersion))
using (IMethodXML mx = mxc.Create())
{
mx.Open(TemplateMethod);
mx.EnableValidation(true);
ListItem[] listItems = ParseList(methodTranList.TransitionList).ToArray();
if (!listItems.Any())
{
throw new IOException("Empty mass list found.");
}
if (InstrumentType.Equals(InstrumentFusion))
{
mx.ApplyMethodModificationsFromXML(GetFusionModificationXml(listItems, outMeth));
}
else
{
mx.ImportMassListFromXML(GetTsqMassListXml(listItems, outMeth));
}
mx.SaveAs(outMeth);
}
if (!File.Exists(outMeth))
{
throw new IOException(string.Format("Failure creating method file {0}.", methodTranList.FinalMethod));
}
}
finally
{
if (!Equals(outMeth, methodTranList.OutputMethod))
{
File.Move(outMeth, methodTranList.OutputMethod);
}
}
}
}
public static string GetSummary(string methodFile, string instrumentModel, string version)
{
methodFile = Path.GetFullPath(methodFile);
using (IMethodXMLContext mxc = CreateContext(instrumentModel, version))
using (IMethodXML xmlMeth = mxc.Create())
{
xmlMeth.Open(methodFile);
return(xmlMeth.GetMethodSummary());
}
}
/// <summary>
/// Validates a .meth file for errors in parameters/settings
/// </summary>
/// <param name="methodFilePath">The method file path</param>
/// <param name="model">The instrument model</param>
/// <param name="version">The instrument version</param>
/// <returns>A list of errors it detected, or an empty list if no errors are found</returns>
public static List <string> Validate(string methodFilePath, string model = "", string version = "")
{
var validationErrors = new List <string>();
methodFilePath = Path.GetFullPath(methodFilePath);
using (IMethodXMLContext mxc = CreateContext(model, version))
using (IMethodXML xmlMeth = mxc.Create())
{
xmlMeth.Open(methodFilePath);
if (!xmlMeth.ValidateMethod())
{
validationErrors.AddRange(xmlMeth.GetLastValidationErrors());
}
}
return(validationErrors);
}
/// <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);
}
}
