// Disabled 20170131 because Skyline Chorus API is offline
// [TestMethod] TODO(nicksh) re-enable when Chorus is reliable
public void TestThermoDIA()
{
if (!RunPerfTests)
{
return; // PerfTests only run when the global "allow perf tests" flag is set
}
var xmlSerializer = new XmlSerializer(typeof(ChromatogramRequestDocument));
var stream = typeof(PerfChorusGenerateChromatograms).Assembly.GetManifestResourceStream(
typeof(PerfChorusGenerateChromatograms), "ThermoDIA.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequestDocument = (ChromatogramRequestDocument)xmlSerializer.Deserialize(stream);
var chorusUrl = TEST_ACCOUNT.GetChorusUrl().SetFileId(28836);
var srmDocument = new SrmDocument(SrmSettingsList.GetDefault());
DateTime startTime = DateTime.Now;
ChromTaskList chromTaskList = new ChromTaskList(() => {}, srmDocument, TEST_ACCOUNT, chorusUrl, new[] { chromatogramRequestDocument });
chromTaskList.SetMinimumSimultaneousTasks(2);
while (chromTaskList.PercentComplete < 100)
{
Thread.Sleep(100);
}
DateTime endTime = DateTime.Now;
AssertEx.AreNoExceptions(chromTaskList.ListExceptions());
Console.Out.WriteLine("Elapsed time {0}", endTime.Subtract(startTime));
}
protected override void DoTest()
{
var chorusAccount = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Hoofnagle_MSe_targeted.sky")));
var importResultsDlg = ShowDialog<ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog<OpenDataSourceDialog>(importResultsDlg.OkDialog);
var multiButtonMsgDlg = ShowDialog<MultiButtonMsgDlg>(() => openDataSourceDialog.CurrentDirectory = ChorusUrl.EMPTY);
OkDialog(multiButtonMsgDlg, multiButtonMsgDlg.Btn1Click);
var editChorusAccountDlg = WaitForOpenForm<EditChorusAccountDlg>();
RunUI(()=>
{
editChorusAccountDlg.SetChorusAccount(chorusAccount);
});
OkDialog(editChorusAccountDlg, editChorusAccountDlg.OkDialog);
Assert.AreEqual(chorusAccount.GetChorusUrl(), openDataSourceDialog.CurrentDirectory);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = chorusAccount.GetChorusUrl().AddPathPart("myFiles");
});
WaitForConditionUI(() => !openDataSourceDialog.WaitingForData);
RunUI(() =>
{
openDataSourceDialog.SelectFile("2013_03_13_UWash_S1_MSE_Adj_001.raw.zip");
openDataSourceDialog.SelectFile("2013_03_13_UWash_S2_MSE_Adj_001.raw.zip");
});
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
ImportResultsNameDlg importResultsNameDlg = WaitForOpenForm<ImportResultsNameDlg>();
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
WaitForConditionUI(() =>
SkylineWindow.DocumentUI.Settings.HasResults &&
SkylineWindow.DocumentUI.Settings.MeasuredResults.IsLoaded
);
Assert.AreEqual(2, SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count);
}
//[TestMethod]
public void TestDdaSmall()
{
ChorusAccount TEST_ACCOUNT = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
var stream = typeof (ChromTaskListTest).Assembly.GetManifestResourceStream(typeof (ChromTaskListTest),
"DdaSmall.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequest = (ChromatogramRequestDocument) new XmlSerializer(typeof (ChromatogramRequestDocument)).Deserialize(stream);
var chromTaskList = new ChromTaskList(() => { }, new SrmDocument(SrmSettingsList.GetDefault()), TEST_ACCOUNT,
TEST_ACCOUNT.GetChorusUrl().SetFileId(28836), ChromTaskList.ChunkChromatogramRequest(chromatogramRequest, 100));
chromTaskList.SetMinimumSimultaneousTasks(10);
var failedTasks = new HashSet<ChromatogramGeneratorTask>();
foreach (var chromKey in chromTaskList.ChromKeys)
{
float[] times;
float[] intensities;
float[] massErrors;
int[] scanIds;
chromTaskList.GetChromatogram(chromKey, out times, out scanIds, out intensities, out massErrors);
if (null == times)
{
var task = chromTaskList.GetGeneratorTask(chromKey);
if (failedTasks.Add(task))
{
var memoryStream = new MemoryStream();
var xmlWriter = XmlWriter.Create(memoryStream, new XmlWriterSettings {Encoding = Encoding.UTF8});
new XmlSerializer(typeof(ChromatogramRequestDocument)).Serialize(xmlWriter, task.ChromatogramRequestDocument);
Console.Out.WriteLine("Failed to get data for {0}", Encoding.UTF8.GetString(memoryStream.ToArray()));
}
}
}
Assert.AreEqual(0, failedTasks.Count);
}
//[TestMethod]
public void TestDdaSmall()
{
ChorusAccount TEST_ACCOUNT = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
var stream = typeof(ChromTaskListTest).Assembly.GetManifestResourceStream(typeof(ChromTaskListTest),
"DdaSmall.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequest = (ChromatogramRequestDocument) new XmlSerializer(typeof(ChromatogramRequestDocument)).Deserialize(stream);
var chromTaskList = new ChromTaskList(() => { }, new SrmDocument(SrmSettingsList.GetDefault()), TEST_ACCOUNT,
TEST_ACCOUNT.GetChorusUrl().SetFileId(28836), ChromTaskList.ChunkChromatogramRequest(chromatogramRequest, 100));
chromTaskList.SetMinimumSimultaneousTasks(10);
var failedTasks = new HashSet <ChromatogramGeneratorTask>();
foreach (var chromKey in chromTaskList.ChromKeys)
{
TimeIntensities timeIntensities;
chromTaskList.GetChromatogram(chromKey, out timeIntensities);
if (null == timeIntensities)
{
var task = chromTaskList.GetGeneratorTask(chromKey);
if (failedTasks.Add(task))
{
var memoryStream = new MemoryStream();
var xmlWriter = XmlWriter.Create(memoryStream, new XmlWriterSettings {
Encoding = Encoding.UTF8
});
new XmlSerializer(typeof(ChromatogramRequestDocument)).Serialize(xmlWriter, task.ChromatogramRequestDocument);
Console.Out.WriteLine("Failed to get data for {0}", Encoding.UTF8.GetString(memoryStream.ToArray()));
}
}
}
Assert.AreEqual(0, failedTasks.Count);
}
protected override void DoTest()
{
var chorusAccount = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Hoofnagle_MSe_targeted.sky")));
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResultsDlg.OkDialog);
var multiButtonMsgDlg = ShowDialog <MultiButtonMsgDlg>(() => openDataSourceDialog.CurrentDirectory = RemoteUrl.EMPTY);
OkDialog(multiButtonMsgDlg, multiButtonMsgDlg.Btn1Click);
var editChorusAccountDlg = WaitForOpenForm <EditRemoteAccountDlg>();
RunUI(() =>
{
editChorusAccountDlg.SetRemoteAccount(chorusAccount);
});
OkDialog(editChorusAccountDlg, editChorusAccountDlg.OkDialog);
Assert.AreEqual(chorusAccount.GetChorusUrl(), openDataSourceDialog.CurrentDirectory);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = chorusAccount.GetChorusUrl().AddPathPart("myFiles");
});
WaitForConditionUI(() => !openDataSourceDialog.WaitingForData);
RunUI(() =>
{
openDataSourceDialog.SelectFile("2013_03_13_UWash_S1_MSE_Adj_001.raw.zip");
openDataSourceDialog.SelectFile("2013_03_13_UWash_S2_MSE_Adj_001.raw.zip");
});
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
ImportResultsNameDlg importResultsNameDlg = WaitForOpenForm <ImportResultsNameDlg>();
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
WaitForConditionUI(() =>
SkylineWindow.DocumentUI.Settings.HasResults &&
SkylineWindow.DocumentUI.Settings.MeasuredResults.IsLoaded
);
Assert.AreEqual(2, SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count);
}