/// <summary>
/// Wrapper class for driving all facets of the analysis pipeline
/// </summary>
/// <param name="MS1MatchFilePath"></param>
/// <param name="glycosylationSiteFilePath"></param>
/// <param name="MS2DeconFilePath"></param>
/// <param name="modelFilePath"></param>
/// <param name="pythonInterpreterPath">
/// Passed along to the ScriptManager, used to locate the Python Interpreter executable
/// </param>
/// <param name="rscriptPath">
/// Passed along to the ScriptManager, used to locate the Rscript executable
/// </param>
/// <param name="scriptsRoot">
/// Passed along to the ScriptManager, used to locate the script pipeline files
/// </param>
public AnalysisPipeline(String MS1MatchFilePath, String glycosylationSiteFilePath,
String MS2DeconFilePath, String modelFilePath = null,
String outputFilePath = null, double ms1MatchingTolerance = 1e-5,
double ms2MatchingTolerance = 2e-5, String proteinProspectorXMLFilePath = null, String method = "full_random_forest",
String pythonInterpreterPath = null, String rscriptPath = null,
String scriptsRoot = null, int numProcesses = 2, bool onlyRandomDecoys = false,
int numDecoys = 20)
{
this.MS1MatchFilePath = MS1MatchFilePath;
this.GlycosylationSiteFilePath = glycosylationSiteFilePath;
this.MS2DeconFilePath = MS2DeconFilePath;
this.ModelFilePath = modelFilePath;
this.ResultFilePath = outputFilePath;
this.ResultsTable = null;
this.State = TandemGlycoPeptideTaskState.New;
this.MS1MatchingTolerance = ms1MatchingTolerance;
this.MS2MatchingTolerance = ms2MatchingTolerance;
this.Method = method;
this.ProteinProspectorXMLFilePath = proteinProspectorXMLFilePath;
this.NumDecoys = numDecoys;
this.NumProcesses = numProcesses;
this.OnlyRandomDecoys = onlyRandomDecoys;
//Make sure that all needed resources can be found
this.Scripter = new ScriptManager(pythonInterpreterPath, rscriptPath, scriptsRoot);
Scripter.VerifyFileSystemTargets();
}
public void ExecuteScriptManagerHelpCall()
{
PythonProcessManager.Verbose = true;
ScriptManager scripter = new ScriptManager();
Assert.IsTrue(scripter.VerifyFileSystemTargets());
Console.WriteLine("Running Dependency Checks");
scripter.InstallPythonDependencies();
}
public void ExecuteScriptManagerRunModelDiagnostics()
{
PythonProcessManager.Verbose = true;
ScriptManager scripter = new ScriptManager();
Assert.IsTrue(scripter.VerifyFileSystemTargets());
Console.WriteLine("Running Model Diagnostics");
String diagnosticOutput = scripter.RunModelDiagnosticTask(ModelJsonFile, "full_random_forest");
Assert.IsTrue(File.Exists(diagnosticOutput));
}
private void CheckPythonDependenciesButton_Click(object sender, EventArgs e)
{
ScriptManager scriptingManager = new ScriptManager(ConfigurationManager.Scripting.PythonInterpreterPath);
try
{
scriptingManager.VerifyFileSystemTargets();
Console.WriteLine("Ping");
scriptingManager.InstallPythonDependencies();
Console.WriteLine("Pong");
ConfigurationManager.Scripting.DependenciesFound = DependencyInstalledState.Yes;
ConfigurationManager.WriteScriptingSettingsToFile(Application.StartupPath, ConfigurationManager.Scripting);
}
catch (Exception ex)
{
ConfigurationManager.Scripting.DependenciesFound = DependencyInstalledState.No;
MessageBox.Show(ex.Message);
}
UpdateDependencyIndicator(ConfigurationManager.Scripting.DependenciesFound);
}
public void TestModelDiagnostics()
{
ScriptManager scripter = new ScriptManager();
String resultsPlotsPath = scripter.RunModelDiagnosticTask(ModelJsonFile, "full_random_forest");
Assert.IsTrue(File.Exists(resultsPlotsPath));
}
private void CSVExportButton_Click(object sender, EventArgs e)
{
openFileDialog1.Filter = "JSON file|*.json";
DialogResult targetFileDialogResult = openFileDialog1.ShowDialog();
if (targetFileDialogResult == DialogResult.OK)
{
try
{
String targetFilePath = openFileDialog1.FileName;
SaveFileDialog fileSaver = new SaveFileDialog();
fileSaver.DefaultExt = "csv";
fileSaver.Filter = "Comma separated volume|*.csv";
fileSaver.FileName = Path.Combine(Path.GetDirectoryName(targetFilePath), Path.GetFileNameWithoutExtension(targetFilePath) + ".csv");
DialogResult resultFileDialog = fileSaver.ShowDialog();
if (resultFileDialog == DialogResult.OK)
{
String resultFileName = fileSaver.FileName;
ScriptManager scripter = new ScriptManager(ConfigurationManager.Scripting.PythonInterpreterPath);
scripter.ConvertToCSV(targetFilePath, resultFileName);
}
}
catch (Exception ex)
{
MessageBox.Show("An error occurred while processing this task: " + ex.Message);
WaitScreen.Close();
}
}
}
static void TestScriptingInstallDependencies()
{
Console.WriteLine("Test Scripting Install Dependencies");
ScriptManager scripter = new ScriptManager(rscriptExecutablePath: Properties.Resources.DevelRscriptPath);
Console.WriteLine(scripter);
scripter.VerifyFileSystemTargets();
scripter.InstallRDependencies();
Console.WriteLine(scripter.LastCall.GenerateDumpMessage());
}