private void ProgressForm_Load(object sender, EventArgs e)
{
var boxShown = false;
foreach (var item in _filesToProcess)
{
var info = new JobInfo();
var textBox = new TextBox
{
Text =
string.Format("{0}{1}{2}{1}Starting...{1}", item, Environment.NewLine,
new string('-', 30)),
Dock = DockStyle.Fill,
Multiline = true,
Tag = info,
ScrollBars = ScrollBars.Vertical
};
if (boxShown)
{
textBox.Visible = false;
}
else
{
textBox.Visible = true;
boxShown = true;
}
ProgressSplit.Panel2.Controls.Add(textBox);
info.updateTextbox = textBox;
JobDataView.Rows.Add(item, 0);
var row = JobDataView.Rows[JobDataView.Rows.Count - 1];
row.Tag = info;
info.rowShown = row;
var runProgram = new MainLogic(info)
{
PercentageUpdate = UpdatePercentage,
LogUpdate = UpdateLog,
StatusUpdate = UpdateBarStatus
};
_tasksRunningList.Add(runProgram);
info.workProcess = runProgram;
string workItem = item;
if (MainForm.IsNetworkSource(item))
{
workItem = _unifiCredentialsByUrl[item].GetUrlWithAuthentication(item);
}
var config = runProgram.ParseCommandLine(_outputFolder, (workItem + "|" + _options).Trim('|'));
runProgram.QueueWork(config);
}
MainLogic.RunQueue();
}
private void ProgressForm_FormClosing(object sender, FormClosingEventArgs e)
{
lock (_cancelMutex)
{
MainLogic.ClearQueue();
foreach (var item in _tasksRunningList)
{
item.ForceExit();
}
}
}
public static void Work()
{
while (true)
{
KeyValuePair <MainLogic, Config> item;
lock (_workQueue)
{
if (!_workQueue.Any())
{
return;
}
item = _workQueue.Dequeue();
}
MainLogic logic = item.Key;
Config config = item.Value;
var LogUpdate = logic.LogUpdate;
var StatusUpdate = logic.StatusUpdate;
var PercentageUpdate = logic.PercentageUpdate;
var _info = logic._info;
try
{
var result = logic.Go(config) == 0 ? 100 : -99;
if (result == 100)
{
if (LogUpdate != null)
{
LogUpdate("Finished.", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Finished", ProgressBarStyle.Continuous, _info);
}
if (PercentageUpdate != null)
{
PercentageUpdate(100, 100, _info);
}
}
else
{
if (LogUpdate != null)
{
LogUpdate("Failed - " + logic._errorMessage, _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Failed", ProgressBarStyle.Continuous, _info);
}
if (PercentageUpdate != null)
{
PercentageUpdate(-99, 100, _info);
}
}
}
catch (Exception e)
{
try
{
if (LogUpdate != null)
{
LogUpdate("Failed - " + e, _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Failed", ProgressBarStyle.Continuous, _info);
}
if (PercentageUpdate != null)
{
PercentageUpdate(-99, 100, _info);
}
}
catch (Exception)
{
//probably nothing left to report to
}
}
}
}
private void ProgressForm_Load(object sender, EventArgs e)
{
var boxShown = false;
foreach (var item in _filesToProcess)
{
var info = new JobInfo();
var textBox = new TextBox
{
Text =
string.Format("{0}{1}{2}{1}Starting...{1}", item, Environment.NewLine,
new string('-', 30)),
Dock = DockStyle.Fill,
Multiline = true,
Tag = info,
ScrollBars = ScrollBars.Vertical
};
if (boxShown)
textBox.Visible = false;
else
{
textBox.Visible = true;
boxShown = true;
}
ProgressSplit.Panel2.Controls.Add(textBox);
info.updateTextbox = textBox;
JobDataView.Rows.Add(item, 0);
var row = JobDataView.Rows[JobDataView.Rows.Count - 1];
row.Tag = info;
info.rowShown = row;
var runProgram = new MainLogic(info)
{
PercentageUpdate = UpdatePercentage,
LogUpdate = UpdateLog,
StatusUpdate = UpdateBarStatus
};
_tasksRunningList.Add(runProgram);
info.workProcess = runProgram;
var config = runProgram.ParseCommandLine(_outputFolder, (item + "|" + _options).Trim('|'));
runProgram.QueueWork(config);
}
MainLogic.RunQueue();
}
public void FilterSubsetTest ()
{
var logicAccessor = new MainLogic(new ProgressForm.JobInfo());
var extension = RunFile(_testPaths.Where(o => o.EndsWith(".mzML")),
logicAccessor,
new string[] { "--filter|\"scanNumber 1-50\"", "--filter|\"scanTime [1.2,4.2]\"", "--filter|\"mzWindow [400,800]\"" },
"mzML");
CompareFiles(extension);
}
public void FilterETDFilterTest ()
{
var logicAccessor = new MainLogic(new ProgressForm.JobInfo());
var extension = RunFile(_testPaths.Where(o => o.EndsWith(".mzML")),
logicAccessor,
new string[] { "--filter|\"msLevel 2-\"", "--filter|\"activation ETD\"", "--filter|\"ETDFilter true true true false 3.1 mz\"" },
"mzML");
CompareFiles(extension);
}
public void FilterActivationTest ()
{
var logicAccessor = new MainLogic(new ProgressForm.JobInfo());
var extension = RunFile(_testPaths,
logicAccessor,
new string[] { "--filter|\"activation ETD\"" },
"mzML");
CompareFiles(extension);
}
public void FilterZeroSamplesTest()
{
var logicAccessor = new MainLogic(new ProgressForm.JobInfo());
var extension = RunFile(_testPaths,
logicAccessor,
new string[] { "--filter|\"zeroSamples removeExtra 1-3\"", "--filter|\"msLevel 1\"" },
"mzML");
CompareFiles(extension);
}
public void FilterPeakPickingTest ()
{
var logicAccessor = new MainLogic(new ProgressForm.JobInfo());
var extension = RunFile(_testPaths,
logicAccessor,
new string[] { "--filter|\"peakPicking true 1\"", "--filter|\"msLevel 1\"" },
"mzML");
CompareFiles(extension);
}
public void Vendor_To_MzML_Test ()
{
var logicAccessor = new MainLogic(new ProgressForm.JobInfo());
var extension = RunFile(_testPaths.Where(o => !o.EndsWith(".mzML")),
logicAccessor,
new string[] { },
"mzML");
CompareFiles(extension);
}
private string RunFile(IEnumerable<string> testPaths, MainLogic logicAccessor, string[] extraArgs, string extension)
{
foreach (string filepath in testPaths)
{
var outputDirectory = Path.GetFileName(filepath);
if (!Directory.Exists(outputDirectory))
Directory.CreateDirectory(outputDirectory);
string[] runIds = ReaderList.FullReaderList.readIds(filepath);
var psi = new ProcessStartInfo(Path.Combine(_workingDirectory, "msconvert.exe"))
{
Arguments = String.Format("{0} --64 --outdir \"{1}\" \"{2}\"",
String.Join(" ", extraArgs).Replace('|', ' '),
outputDirectory,
filepath),
UseShellExecute = false,
CreateNoWindow = true
};
var proc = new Process { StartInfo = psi };
// start console conversion
proc.Start();
proc.WaitForExit();
foreach (string runId in runIds)
{
var outputFilepath = Directory.GetFiles(outputDirectory, "*" + runId + "." + extension).First();
var consoleOutput = Path.ChangeExtension(outputFilepath, ".console." + extension);
Assert.IsTrue(File.Exists(outputFilepath), "Console result file not found");
File.Move(outputFilepath, consoleOutput);
}
// start GUI conversion
var config = logicAccessor.ParseCommandLine(outputDirectory, String.Format("{0}|{1}", String.Join("|", extraArgs).Replace("\"", String.Empty), filepath).Trim('|'));
logicAccessor.QueueWork(config);
MainLogic.Work();
foreach (string runId in runIds)
{
var outputFilepath = Directory.GetFiles(outputDirectory, "*" + runId + "." + extension).First();
var guiOutput = Path.ChangeExtension(outputFilepath, ".gui." + extension);
Assert.IsTrue(File.Exists(outputFilepath), "GUI result file not found");
File.Move(outputFilepath, guiOutput);
}
}
return extension;
}
