public void TestSkylineRunnerArgs()
{
const string skyFile = @"C:\Dummy\path\Test_file.sky";
const string dataFile1 = @"C:\Dummy\path\Test1.raw";
var logger = new TestLogger();
var mainSettings = new MainSettings()
{
SkylineFilePath = skyFile,
ResultsWindowString = MainSettings.ACCUM_TIME_WINDOW.ToString()
};
var mainSettingsTab = new MainSettingsTab(null, logger)
{
Settings = mainSettings
};
var accumulationWindow = MainSettingsTab.AccumulationWindow.Get(DateTime.Now, MainSettings.ACCUM_TIME_WINDOW);
Assert.AreEqual(accumulationWindow.EndDate.Subtract(accumulationWindow.StartDate).Days + 1,
MainSettings.ACCUM_TIME_WINDOW);
var expected =
string.Format("--in=\"{0}\" --remove-before={1} --import-file=\"{3}\" --import-on-or-after={2} --save", skyFile,
accumulationWindow.StartDate.ToShortDateString(),
accumulationWindow.StartDate.ToShortDateString(), dataFile1);
var importContext = new ImportContext(dataFile1);
Assert.IsFalse(importContext.ImportExisting);
var args = mainSettingsTab.SkylineRunnerArgs(importContext);
Assert.AreEqual(expected, args.Trim());
}
public void TestBackgroundWorker_ProcessNewFiles()
{
// Create a test directory to monitor
var dir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
Assert.IsNotNull(dir);
var testDir = Path.Combine(dir, "TestBackgroundWorker");
if (Directory.Exists(testDir))
{
Directory.Delete(testDir, true);
}
Assert.IsFalse(Directory.Exists(testDir));
Directory.CreateDirectory(testDir);
Assert.IsTrue(Directory.Exists(testDir));
var appControl = new TestAppControl();
var logger = new TestLogger();
var processControl = new TestProcessControl(logger);
var mainSettings = new MainSettings
{
FolderToWatch = testDir,
InstrumentType = "NoInstrument",
ResultsWindowString = "31",
AcquisitionTimeString = "0"
};
// Start the background worker.
var backgroundWorker = new AutoQCBackgroundWorker(appControl, processControl, logger);
backgroundWorker.Start(mainSettings);
Assert.IsTrue(backgroundWorker.IsRunning());
// Create a new file in the test directory.
Thread.Sleep(1000);
CreateNewFile(testDir, "test1.txt");
// Wait till the the file has been processed.
while (!processControl.IsDone())
{
Thread.Sleep(500);
}
Assert.IsTrue(backgroundWorker.IsRunning());
// Create another file in the test directory.
Thread.Sleep(1000);
CreateNewFile(testDir, "test2.txt");
// Wait till the the file has been processed.
// Process4 returns exit code 1 both times. This should stop the program.
while (!processControl.IsDone())
{
Thread.Sleep(500);
}
// Assert.IsTrue(appControl.Waiting);
Thread.Sleep(2 * AutoQCBackgroundWorker.WAIT_5SEC);
Assert.IsTrue(appControl.Stopped);
Assert.AreEqual(Regex.Replace(logger.GetLog(), @"\s+", ""),
Regex.Replace(GetExpectedLog_ProcessNew(), @"\s+", ""));
}
private static IResultFileStatus GetFileStatusChecker(MainSettings mainSettings)
{
if (mainSettings.InstrumentType.Equals(MainSettings.THERMO))
{
return(new XRawFileStatus(mainSettings.AcquisitionTime));
}
return(new AcquisitionTimeFileStatus(mainSettings.AcquisitionTime));
}
public void TestGetLastArchivalDate()
{
var mainSettings = new MainSettings() { SkylineFilePath = @"C:\Dummy\path\Test_file.sky" };
var mainSettingsTab = new MainSettingsTab(null, null) {Settings = mainSettings};
var fsUtil = new TestFileSystemUtil();
Assert.AreEqual(new DateTime(2015, 06, 01), mainSettingsTab.GetLastArchivalDate(fsUtil));
}
public void Validate()
{
if (string.IsNullOrEmpty(Name))
{
throw new ArgumentException("Please enter a name for the configuration.");
}
MainSettings.ValidateSettings();
PanoramaSettings.ValidateSettings();
}
public static AutoQcConfig GetDefault()
{
var config = new AutoQcConfig
{
MainSettings = MainSettings.GetDefault(),
PanoramaSettings = PanoramaSettings.GetDefault()
};
return(config);
}
public AutoQcConfig Copy()
{
return(new AutoQcConfig
{
Name = Name,
IsEnabled = false, // Disable by default
User = PanoramaSettings.PanoramaUserEmail,
MainSettings = MainSettings.Copy(),
PanoramaSettings = PanoramaSettings.Copy()
});
}
public override int GetHashCode()
{
unchecked
{
var hashCode = (Name != null ? Name.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ IsEnabled.GetHashCode();
hashCode = (hashCode * 397) ^ (MainSettings != null ? MainSettings.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (PanoramaSettings != null ? PanoramaSettings.GetHashCode() : 0);
return(hashCode);
}
}
protected bool Equals(MainSettings other)
{
return(string.Equals(SkylineFilePath, other.SkylineFilePath) &&
string.Equals(FolderToWatch, other.FolderToWatch) &&
IncludeSubfolders == other.IncludeSubfolders &&
Equals(QcFileFilter, other.QcFileFilter) &&
ResultsWindow == other.ResultsWindow &&
string.Equals(InstrumentType, other.InstrumentType) &&
AcquisitionTime == other.AcquisitionTime &&
LastAcquiredFileDate.Equals(other.LastAcquiredFileDate));
}
public void WriteXml(XmlWriter writer)
{
writer.WriteStartElement("autoqc_config");
writer.WriteAttribute(ATTR.name, Name);
writer.WriteAttributeIfString(ATTR.user, User);
writer.WriteAttributeIfString(ATTR.created, Created.ToShortDateString() + " " + Created.ToShortTimeString());
writer.WriteAttributeIfString(ATTR.modified, Modified.ToShortDateString() + " " + Modified.ToShortTimeString());
MainSettings.WriteXml(writer);
PanoramaSettings.WriteXml(writer);
writer.WriteEndElement();
}
public void SetUIMainSettings(MainSettings mainSettings)
{
RunUI(() =>
{
textSkylinePath.Text = mainSettings.SkylineFilePath;
textFolderToWatchPath.Text = mainSettings.FolderToWatch;
textResultsTimeWindow.Text = mainSettings.ResultsWindowString;
textAquisitionTime.Text = mainSettings.AcquisitionTimeString;
comboBoxInstrumentType.SelectedItem = mainSettings.InstrumentType;
comboBoxInstrumentType.SelectedIndex = comboBoxInstrumentType.FindStringExact(mainSettings.InstrumentType);
});
}
public static MainSettings GetDefault()
{
var settings = new MainSettings
{
InstrumentType = THERMO,
ResultsWindow = ACCUM_TIME_WINDOW,
AcquisitionTime = ACQUISITION_TIME,
QcFileFilter = FileFilter.GetFileFilter(AllFileFilter.NAME, string.Empty)
};
return(settings);
}
private MainSettings GetMainSettingsFromUI()
{
var mainSettings = new MainSettings()
{
SkylineFilePath = textSkylinePath.Text,
FolderToWatch = textFolderToWatchPath.Text,
ResultsWindowString = textResultsTimeWindow.Text,
InstrumentType = comboBoxInstrumentType.SelectedItem.ToString(),
AcquisitionTimeString = textAquisitionTime.Text
};
return(mainSettings);
}
private MainSettings GetMainSettingsFromUI()
{
var mainSettings = new MainSettings();
mainSettings.SkylineFilePath = textSkylinePath.Text;
mainSettings.FolderToWatch = textFolderToWatchPath.Text;
mainSettings.IncludeSubfolders = includeSubfoldersCb.Checked;
mainSettings.QcFileFilter = FileFilter.GetFileFilter(comboBoxFileFilter.SelectedItem.ToString(),
textQCFilePattern.Text);
mainSettings.ResultsWindow = ValidateIntTextField(textResultsTimeWindow.Text, "Results Window");
mainSettings.InstrumentType = comboBoxInstrumentType.SelectedItem.ToString();
mainSettings.AcquisitionTime = ValidateIntTextField(textAquisitionTime.Text, "Acquisition Time");
return(mainSettings);
}
public bool IsIntegrateAllChecked(IAutoQcLogger logger, MainSettings mainSettings)
{
try
{
using (var stream = new FileStream(mainSettings.SkylineFilePath, FileMode.Open))
{
using (XmlReader reader = XmlReader.Create(stream))
{
reader.MoveToContent();
var done = false;
while (reader.Read() && !done)
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
if (reader.Name == "transition_integration")
{
if (reader.MoveToAttribute("integrate_all"))
{
bool integrateAll;
Boolean.TryParse(reader.Value, out integrateAll);
return(integrateAll);
}
done = true;
}
break;
case XmlNodeType.EndElement:
if (reader.Name.Equals("transition_settings")) // We have come too far
{
done = true;
}
break;
}
}
}
}
}
catch (Exception e)
{
logger.LogException(e, "Error reading file {0}.", mainSettings.SkylineFilePath);
return(false);
}
logger.LogError("\"Integrate all\" is not checked for the Skyline document. This setting is under the \"Settings\" menu in Skyline, and should be checked for " +
" documents with QC results.");
return(false);
}
private void SetUIMainSettings(MainSettings mainSettings)
{
RunUI(() =>
{
textSkylinePath.Text = mainSettings.SkylineFilePath;
textFolderToWatchPath.Text = mainSettings.FolderToWatch;
includeSubfoldersCb.Checked = mainSettings.IncludeSubfolders;
textQCFilePattern.Text = mainSettings.QcFileFilter.Pattern;
comboBoxFileFilter.SelectedItem = mainSettings.QcFileFilter.Name();
textResultsTimeWindow.Text = mainSettings.ResultsWindow.ToString();
textAquisitionTime.Text = mainSettings.AcquisitionTime.ToString();
comboBoxInstrumentType.SelectedItem = mainSettings.InstrumentType;
comboBoxInstrumentType.SelectedIndex = comboBoxInstrumentType.FindStringExact(mainSettings.InstrumentType);
});
}
public void Init(MainSettings mainSettings)
{
_dataFiles = new ConcurrentQueue <string>();
_retryFiles = new Queue <RawFile>();
_fileStatusChecker = GetFileStatusChecker(mainSettings);
_fileWatcher.EnableRaisingEvents = false;
_fileWatcher.Filter = GetFileFilter(mainSettings.InstrumentType, out _dataInDirectories);
_fileWatcher.Path = mainSettings.FolderToWatch;
_acquisitionTimeSetting = mainSettings.AcquisitionTime;
}
public static MainSettings InitializeFromDefaults()
{
var settings = new MainSettings
{
SkylineFilePath = Settings.Default.SkylineFilePath,
FolderToWatch = Settings.Default.FolderToWatch,
};
var accumWin = Settings.Default.ResultsWindow;
settings.ResultsWindowString = accumWin == 0 ? ACCUM_TIME_WINDOW.ToString() : accumWin.ToString();
var instrumentType = Settings.Default.InstrumentType;
settings.InstrumentType = string.IsNullOrEmpty(instrumentType) ? THERMO : instrumentType;
var acquisitionTime = Settings.Default.AcquisitionTime;
settings.AcquisitionTimeString = acquisitionTime == 0 ? ACQUISITION_TIME.ToString() : acquisitionTime.ToString();
return(settings);
}
public void ReadXml(XmlReader reader)
{
Name = reader.GetAttribute(ATTR.name);
// TODO: Configurations shouldn't start automatically when the program starts up.
// Remove this attribute from the config XML?
IsEnabled = false; // reader.GetBoolAttribute(ATTR.is_enabled);
User = reader.GetAttribute(ATTR.user);
DateTime dateTime;
DateTime.TryParse(reader.GetAttribute(ATTR.created), out dateTime);
Created = dateTime;
DateTime.TryParse(reader.GetAttribute(ATTR.modified), out dateTime);
Modified = dateTime;
do
{
reader.Read();
} while (reader.NodeType != XmlNodeType.Element);
var mainSettings = new MainSettings();
mainSettings.ReadXml(reader);
MainSettings = mainSettings;
do
{
reader.Read();
} while (reader.NodeType != XmlNodeType.Element);
var panoramaSettings = new PanoramaSettings();
panoramaSettings.ReadXml(reader);
PanoramaSettings = panoramaSettings;
do
{
reader.Read();
} while (reader.NodeType != XmlNodeType.EndElement);
}
public void TestAddArchiveArgs()
{
var mainSettings = new MainSettings() { SkylineFilePath = @"C:\Dummy\path\Test_file.sky" };
var mainSettingsTab = new MainSettingsTab(null, new TestLogger()) {Settings = mainSettings};
var date = new DateTime(2015, 6, 17);
mainSettingsTab.LastArchivalDate = date;
var args = mainSettingsTab.GetArchiveArgs(mainSettingsTab.LastArchivalDate, date);
Assert.IsNull(args);
Assert.AreEqual(date, mainSettingsTab.LastArchivalDate);
date = date.AddMonths(1); // 07/17/2015
var archiveArg = string.Format("--share-zip={0}", "Test_file_2015_06.sky.zip");
args = mainSettingsTab.GetArchiveArgs(mainSettingsTab.LastArchivalDate, date);
Assert.AreEqual(archiveArg, args);
Assert.AreEqual(date, mainSettingsTab.LastArchivalDate);
date = date.AddYears(1); // 06/17/2016
archiveArg = string.Format("--share-zip={0}", "Test_file_2015_07.sky.zip");
args = mainSettingsTab.GetArchiveArgs(mainSettingsTab.LastArchivalDate, date);
Assert.AreEqual(archiveArg, args);
Assert.AreEqual(date, mainSettingsTab.LastArchivalDate);
}
public void ReadXml(XmlReader reader)
{
Name = reader.GetAttribute(ATTR.name);
IsEnabled = reader.GetBoolAttribute(ATTR.is_enabled);
User = reader.GetAttribute(ATTR.user);
DateTime dateTime;
DateTime.TryParse(reader.GetAttribute(ATTR.created), out dateTime);
Created = dateTime;
DateTime.TryParse(reader.GetAttribute(ATTR.modified), out dateTime);
Modified = dateTime;
do
{
reader.Read();
} while (reader.NodeType != XmlNodeType.Element);
var mainSettings = new MainSettings();
mainSettings.ReadXml(reader);
MainSettings = mainSettings;
do
{
reader.Read();
} while (reader.NodeType != XmlNodeType.Element);
var panoramaSettings = new PanoramaSettings();
panoramaSettings.ReadXml(reader);
PanoramaSettings = panoramaSettings;
do
{
reader.Read();
} while (reader.NodeType != XmlNodeType.EndElement);
}
public void Init(MainSettings mainSettings)
{
_dataFiles = new ConcurrentQueue<string>();
_retryFiles = new Queue<RawFile>();
_fileStatusChecker = GetFileStatusChecker(mainSettings);
_fileWatcher.EnableRaisingEvents = false;
_fileWatcher.Filter = GetFileFilter(mainSettings.InstrumentType);
_fileWatcher.Path = mainSettings.FolderToWatch;
_acquisitionTimeSetting = mainSettings.AcquisitionTime;
}
private static IResultFileStatus GetFileStatusChecker(MainSettings mainSettings)
{
if (mainSettings.InstrumentType.Equals(MainSettings.THERMO))
{
return new XRawFileStatus(mainSettings.AcquisitionTime);
}
return new AcquisitionTimeFileStatus(mainSettings.AcquisitionTime);
}
public override bool ValidateSettings()
{
LogOutput("Validating settings...");
var mainSettingsUI = _appControl.GetUIMainSettings();
var error = false;
// Path to the Skyline file.
var path = mainSettingsUI.SkylineFilePath;
if (string.IsNullOrWhiteSpace(path))
{
LogErrorOutput("Please specify path to a Skyline file.");
error = true;
}
else if (!File.Exists(path))
{
LogErrorOutput("Skyline file {0} does not exist.", path);
error = true;
}
// Path to the folder to monitor for mass spec. results files
path = mainSettingsUI.FolderToWatch;
if (string.IsNullOrWhiteSpace(path))
{
LogErrorOutput("Please specify path to a folder where mass spec. files will be written.");
error = true;
}
else if (!Directory.Exists(path))
{
LogErrorOutput("Folder {0} does not exist.", path);
error = true;
}
// Results time window.
var accumWin = mainSettingsUI.ResultsWindowString;
if (string.IsNullOrWhiteSpace(accumWin))
{
LogErrorOutput("Please specify a value for the \"Accumulation time window\".");
error = true;
}
else
{
int accumWindow;
if (!Int32.TryParse(mainSettingsUI.ResultsWindowString, out accumWindow))
{
LogErrorOutput("Invalid value for \"Accumulation time window\": {0}.",
mainSettingsUI.ResultsWindowString);
error = true;
}
else if (accumWindow < MainSettings.ACCUM_TIME_WINDOW)
{
LogErrorOutput("\"Accumulation time window\" cannot be less than {0} days.", MainSettings.ACCUM_TIME_WINDOW);
error = true;
}
}
// Expected acquisition time
var aquisitionTime = mainSettingsUI.AcquisitionTimeString;
if (string.IsNullOrWhiteSpace(aquisitionTime))
{
LogErrorOutput("Please specify a value for the \"Expected acquisition time\".");
error = true;
}
else
{
int aAcquisitionTime;
if (!Int32.TryParse(mainSettingsUI.AcquisitionTimeString, out aAcquisitionTime))
{
LogErrorOutput("Invalid value for \"Expected acquisition time\": {0}.",
mainSettingsUI.AcquisitionTimeString);
error = true;
}
}
if (!error) Settings = mainSettingsUI;
return !error;
}
public void TestValidateSettings()
{
var logger = new TestLogger();
var mainControl = new TestAppControl();
var mainSettingsTab = new MainSettingsTab(mainControl, logger);
Assert.IsFalse(mainSettingsTab.ValidateSettings());
var log = logger.GetLog();
Assert.IsTrue(log.Contains("Please specify path to a Skyline file."));
Assert.IsTrue(log.Contains("Please specify path to a folder where mass spec. files will be written."));
Assert.IsTrue(log.Contains("Please specify a value for the \"Accumulation time window\"."));
const string skyPath = "C:\\dummy\\path\\Test.sky";
const string folderPath = "C:\\dummy\\path";
var accumWindow = "not a number";
var settings = new MainSettings()
{
SkylineFilePath = skyPath,
FolderToWatch = folderPath,
ResultsWindowString = "not a number",
// ImportExistingFiles = false
};
mainControl = new TestAppControl();
mainControl.SetUIMainSettings(settings);
mainSettingsTab = new MainSettingsTab(mainControl, logger);
logger.Clear();
Assert.IsFalse(mainSettingsTab.ValidateSettings());
log = logger.GetLog();
Assert.IsTrue(log.Contains(string.Format("Skyline file {0} does not exist.", skyPath)));
Assert.IsTrue(log.Contains(string.Format("Folder {0} does not exist.", folderPath)));
Assert.IsTrue(log.Contains(string.Format("Invalid value for \"Accumulation time window\": {0}.", accumWindow)));
accumWindow = "-1";
settings.ResultsWindowString = accumWindow;
logger.Clear();
mainSettingsTab = new MainSettingsTab(mainControl, logger);
Assert.IsFalse(mainSettingsTab.ValidateSettings());
log = logger.GetLog();
Assert.IsTrue(
log.Contains(string.Format("\"Accumulation time window\" cannot be less than {0} days.",
MainSettings.ACCUM_TIME_WINDOW)));
}
public MainSettingsTab(IAppControl appControl, IAutoQCLogger logger)
: base(appControl, logger)
{
Settings = new MainSettings();
}
private static IResultFileStatus GetFileStatusChecker(MainSettings mainSettings)
{
return(new AcquisitionTimeFileStatus(mainSettings.AcquisitionTime));
}
public override void InitializeFromDefaultSettings()
{
Settings = MainSettings.InitializeFromDefaults();
_appControl.SetUIMainSettings(Settings);
}
public void TestSkylineRunnerArgsImportExisting()
{
const string skyFile = @"C:\Dummy\path\Test_file.sky";
const string dataFile1 = @"C:\Dummy\path\Test1.raw";
const string dataFile2 = @"C:\Dummy\path\Test2.raw";
var logger = new TestLogger();
var mainSettings = new MainSettings()
{
SkylineFilePath = skyFile,
ResultsWindowString = MainSettings.ACCUM_TIME_WINDOW.ToString()
};
var mainSettingsTab = new MainSettingsTab(null, logger)
{
Settings = mainSettings
};
// Create an import context.
var importContext = new ImportContext(new List<string>() { dataFile1, dataFile2 });
Assert.IsTrue(importContext.ImportExisting);
// Arguments for the first file.
var expected =
string.Format("--in=\"{0}\" --import-file=\"{1}\" --save", skyFile, dataFile1);
importContext.GetNextFile();
var args = mainSettingsTab.SkylineRunnerArgs(importContext);
Assert.AreEqual(expected, args.Trim());
// Arguments for the second file
importContext.GetNextFile();
Assert.IsTrue(importContext.ImportingLast());
expected =
string.Format("--in=\"{0}\" --import-file=\"{1}\" --save", skyFile, dataFile2);
args = mainSettingsTab.SkylineRunnerArgs(importContext);
Assert.AreEqual(expected, args.Trim());
Assert.IsNull(importContext.GetNextFile());
}
public override void InitializeFromDefaultSettings()
{
Settings = MainSettings.InitializeFromDefaults();
_appControl.SetUIMainSettings(Settings);
}
public void Start(MainSettings mainSettings)
{
_lastAcquiredFileDate = mainSettings.LastAcquiredFileDate;
_fileWatcher.Init(mainSettings);
ProcessFiles();
}
public void SetUIMainSettings(MainSettings mainSettings)
{
_mainSettings = mainSettings;
}
public static MainSettings InitializeFromDefaults()
{
var settings = new MainSettings
{
SkylineFilePath = Settings.Default.SkylineFilePath,
FolderToWatch = Settings.Default.FolderToWatch,
};
var accumWin = Settings.Default.ResultsWindow;
settings.ResultsWindowString = accumWin == 0 ? ACCUM_TIME_WINDOW.ToString() : accumWin.ToString();
var instrumentType = Settings.Default.InstrumentType;
settings.InstrumentType = string.IsNullOrEmpty(instrumentType) ? THERMO : instrumentType;
var acquisitionTime = Settings.Default.AcquisitionTime;
settings.AcquisitionTimeString = acquisitionTime == 0 ? ACQUISITION_TIME.ToString() : acquisitionTime.ToString();
return settings;
}
public void Start(MainSettings mainSettings)
{
_lastAcquiredFileDate = mainSettings.LastAcquiredFileDate;
_fileWatcher.Init(mainSettings);
ProcessFiles();
}
public MainSettingsTab(IAppControl appControl, IAutoQCLogger logger)
: base(appControl, logger)
{
Settings = new MainSettings();
}
