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+", ""));
}
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 TestValidatePanoramaSettings()
{
var logger = new TestLogger();
var settings = new PanoramaSettings();
var mainControl = new TestAppControl();
mainControl.SetUIPanoramaSettings(settings);
var panoramaSettingsTab = new PanoramaSettingsTab(mainControl, logger);
Assert.IsTrue(panoramaSettingsTab.ValidateSettings());
var log = logger.GetLog();
Assert.IsTrue(log.Contains("Will NOT publish Skyline documents to Panorama."));
settings.PublishToPanorama = true;
logger.Clear();
panoramaSettingsTab.Settings = settings;
Assert.IsFalse(panoramaSettingsTab.ValidateSettings());
log = logger.GetLog();
Assert.IsTrue(log.Contains("Please specify a Panorama server URL."));
Assert.IsTrue(log.Contains("Please specify a Panorama login name."));
Assert.IsTrue(log.Contains("Please specify a Panorama user password."));
Assert.IsTrue(log.Contains("Please specify a folder on the Panorama server."));
}
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 = MainSettings.GetDefault();
mainSettings.FolderToWatch = testDir;
mainSettings.InstrumentType = "NoInstrument";
AutoQcConfig config = new AutoQcConfig();
config.MainSettings = mainSettings;
config.PanoramaSettings = PanoramaSettings.GetDefault();
config.Name = "Test Config";
config.IsEnabled = true;
var configRunner = new ConfigRunner(config, appControl);
// Start the background worker.
// configRunner.Start();
//Thread.Sleep(1000);
// Assert.IsTrue(configRunner.IsBusy());
// 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(configRunner.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. This should put the file in the re-import queue.
// while (!processControl.IsDone())
// {
// Thread.Sleep(500);
// }
//
// // Assert.IsTrue(appControl.Waiting);
// Thread.Sleep(2 * AutoQCBackgroundWorker.WAIT_FOR_NEW_FILE);
// //Assert.IsTrue(appControl.Waiting);
//
// Assert.AreEqual(Regex.Replace(logger.GetLog(), @"\s+", ""),
// Regex.Replace(GetExpectedLog_ProcessNew(), @"\s+", ""));
}
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 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());
}
private static void TestGetNewFilesForInstrument(string testDir, string instrument)
{
var logger = new TestLogger();
IConfigRunner configRunner = new TestConfigRunner();
configRunner.ChangeStatus(ConfigRunner.RunnerStatus.Running);
// folder to watch
var folderToWatch = CreateDirectory(testDir, instrument);
// Create a .sky files
var skyFile = CreateFile(folderToWatch, "test2_a.sky");
var config = new AutoQcConfig();
// 1. Look for files in folderToWatchOnly
var watcher = new AutoQCFileSystemWatcher(logger, configRunner);
var defaultFileFilter = FileFilter.GetFileFilter(AllFileFilter.NAME, string.Empty);
var mainSettings = new MainSettings(skyFile, folderToWatch, false, defaultFileFilter, true,
MainSettings.ACCUM_TIME_WINDOW, instrument, MainSettings.ACQUISITION_TIME);
config.MainSettings = mainSettings;
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
// Create new files in the folder
List <string> dataFiles;
SetupTestFolder(folderToWatch, instrument, out dataFiles);
// Only one file should have been added to the queue since we are not monitoring sub-folders
Assert.AreEqual(1, watcher.GetExistingFiles().Count);
var files = new List <string>();
string f;
while ((f = watcher.GetFile()) != null)
{
files.Add(f);
}
Assert.AreEqual(1, files.Count);
Assert.IsTrue(files.Contains(dataFiles[0]));
Assert.IsNull(watcher.GetFile()); // Nothing in the queue
watcher.Stop();
// 2. Look for files in subfolders
watcher = new AutoQCFileSystemWatcher(logger, configRunner);
// folder to watch
folderToWatch = CreateDirectory(testDir, instrument + "_2");
// Create a .sky files
skyFile = CreateFile(folderToWatch, "test2_b.sky");
// mainSettings.IncludeSubfolders = true; // watch sub-folders
mainSettings = new MainSettings(skyFile, folderToWatch, true, defaultFileFilter, true,
MainSettings.ACCUM_TIME_WINDOW, instrument, MainSettings.ACQUISITION_TIME);
config.MainSettings = mainSettings;
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
dataFiles.Clear();
SetupTestFolder(folderToWatch, instrument, out dataFiles); // Create new files in the folder
files = new List <string>();
while ((f = watcher.GetFile()) != null)
{
files.Add(f);
}
Assert.AreEqual(5, files.Count);
Assert.IsTrue(files.Contains(dataFiles[0]));
Assert.IsTrue(files.Contains(dataFiles[1]));
Assert.IsTrue(files.Contains(dataFiles[2]));
Assert.IsTrue(files.Contains(dataFiles[3]));
Assert.IsTrue(files.Contains(dataFiles[4]));
watcher.Stop();
// 3. Look for files in subfolders matching a pattern
watcher = new AutoQCFileSystemWatcher(logger, configRunner);
// folder to watch
folderToWatch = CreateDirectory(testDir, instrument + "_3");
// Create a .sky files
skyFile = CreateFile(folderToWatch, "test2_c.sky");
// mainSettings.IncludeSubfolders = true; // watch sub-folders
var fileFilter = FileFilter.GetFileFilter(ContainsFilter.NAME, "_QC_"); // file name pattern
mainSettings = new MainSettings(skyFile, folderToWatch, true, fileFilter, true,
MainSettings.ACCUM_TIME_WINDOW, instrument, MainSettings.ACQUISITION_TIME);
config.MainSettings = mainSettings;
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
dataFiles.Clear();
SetupTestFolder(folderToWatch, instrument, out dataFiles); // Create new files in the folder
files = new List <string>();
while ((f = watcher.GetFile()) != null)
{
files.Add(f);
}
Assert.AreEqual(2, files.Count);
Assert.IsTrue(files.Contains(dataFiles[0]));
Assert.IsTrue(files.Contains(dataFiles[2]));
watcher.Stop();
// 4. Add new files in directory by first creating a temp file/directory and renaming it.
// This should trigger a "Renamed" event for the FileSystemWatcher
watcher = new AutoQCFileSystemWatcher(logger, configRunner);
// folder to watch
folderToWatch = CreateDirectory(testDir, instrument + "_4");
// Create a .sky files
skyFile = CreateFile(folderToWatch, "test2_d.sky");
mainSettings = new MainSettings(skyFile, folderToWatch, false, defaultFileFilter, true,
MainSettings.ACCUM_TIME_WINDOW, instrument, MainSettings.ACQUISITION_TIME);
config.MainSettings = mainSettings;
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
dataFiles.Clear();
SetupTestFolder(folderToWatch, instrument, out dataFiles,
true); // Create temp file first and rename it
watcher.CheckDrive(); // Otherwise UNC tests might fail on //net-lab3
files = new List <string>();
while ((f = watcher.GetFile()) != null)
{
files.Add(f);
}
Assert.AreEqual(1, files.Count);
Assert.IsTrue(files.Contains(dataFiles[0]));
watcher.Stop();
}
private static void TestGetNewFilesForInstrument(string testDir, string instrument)
{
var logger = new TestLogger();
// folder to watch
var folderToWatch = CreateDirectory(testDir, instrument);
// Create a .sky files
var skyFile = CreateFile(folderToWatch, "test2_a.sky");
var config = new AutoQcConfig();
// 1. Look for files in folderToWatchOnly
var watcher = new AutoQCFileSystemWatcher(logger);
var mainSettings = MainSettings.GetDefault();
config.MainSettings = mainSettings;
mainSettings.SkylineFilePath = skyFile;
mainSettings.IncludeSubfolders = false;
mainSettings.InstrumentType = instrument;
mainSettings.FolderToWatch = folderToWatch;
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
// Create new files in the folder
List <string> dataFiles;
SetupTestFolder(folderToWatch, instrument, out dataFiles);
// Only one file should have been added to the queue since we are not monitoring sub-folders
Assert.IsNotNull(watcher.GetFile());
Assert.IsNull(watcher.GetFile());
watcher.Stop();
// 2. Look for files in subfolders
watcher = new AutoQCFileSystemWatcher(logger);
// folder to watch
folderToWatch = CreateDirectory(testDir, instrument + "_2");
// Create a .sky files
skyFile = CreateFile(folderToWatch, "test2_b.sky");
mainSettings.SkylineFilePath = skyFile;
mainSettings.InstrumentType = instrument;
mainSettings.FolderToWatch = folderToWatch;
mainSettings.IncludeSubfolders = true; // watch sub-folders
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
dataFiles.Clear();
SetupTestFolder(folderToWatch, instrument, out dataFiles); // Create new files in the folder
var files = new List <string>();
string f;
while ((f = watcher.GetFile()) != null)
{
files.Add(f);
}
Assert.AreEqual(5, files.Count);
Assert.IsTrue(files.Contains(dataFiles[0]));
Assert.IsTrue(files.Contains(dataFiles[1]));
Assert.IsTrue(files.Contains(dataFiles[2]));
Assert.IsTrue(files.Contains(dataFiles[3]));
Assert.IsTrue(files.Contains(dataFiles[4]));
// 3. Look for files in subfolders matching a pattern
watcher = new AutoQCFileSystemWatcher(logger);
// folder to watch
folderToWatch = CreateDirectory(testDir, instrument + "_3");
// Create a .sky files
skyFile = CreateFile(folderToWatch, "test2_c.sky");
mainSettings.SkylineFilePath = skyFile;
mainSettings.InstrumentType = instrument;
mainSettings.FolderToWatch = folderToWatch;
mainSettings.IncludeSubfolders = true; // watch sub-folders
mainSettings.QcFileFilter = FileFilter.GetFileFilter(ContainsFilter.NAME, "_QC_"); // file name pattern
mainSettings.ValidateSettings();
watcher.Init(config);
watcher.StartWatching(); // Start watching
Assert.AreEqual(0, watcher.GetExistingFiles().Count); // No existing files
dataFiles.Clear();
SetupTestFolder(folderToWatch, instrument, out dataFiles); // Create new files in the folder
files = new List <string>();
while ((f = watcher.GetFile()) != null)
{
files.Add(f);
}
Assert.AreEqual(2, files.Count);
Assert.IsTrue(files.Contains(dataFiles[0]));
Assert.IsTrue(files.Contains(dataFiles[2]));
}