public override bool GetChromatogram(
int id,
Target modifiedSequence,
Color peptideColor,
out ChromExtra extra,
out TimeIntensities timeIntensities)
{
bool loaded = false;
extra = null;
timeIntensities = null;
int idRemain = id;
for (int iTaskList = 0; iTaskList < _chromatogramRequestProviders.Length; iTaskList++)
{
ChromatogramRequestProvider requestProvider = _chromatogramRequestProviders[iTaskList];
if (requestProvider.ChromKeys.Count <= idRemain)
{
idRemain -= requestProvider.ChromKeys.Count;
continue;
}
ChromTaskList chromTaskList = _chromTaskLists[iTaskList];
if (null == chromTaskList)
{
chromTaskList = _chromTaskLists[iTaskList] = new ChromTaskList(CheckCancelled, _document, _chorusAccount, requestProvider.ChorusUrl, ChromTaskList.ChunkChromatogramRequest(requestProvider.GetChromatogramRequest(), 1000));
chromTaskList.SetMinimumSimultaneousTasks(3);
}
ChromKey chromKey = requestProvider.ChromKeys[idRemain];
loaded = chromTaskList.GetChromatogram(chromKey, out timeIntensities);
if (loaded)
{
extra = new ChromExtra(id, chromKey.Precursor == 0 ? 0 : -1);
if (chromKey.Precursor.IsNegative)
{
_sourceHasNegativePolarityData = true;
}
else
{
_sourceHasPositivePolarityData = true;
}
if (timeIntensities.NumPoints > 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
extra.StatusId,
extra.StatusRank,
timeIntensities.Times,
timeIntensities.Intensities);
}
}
break;
}
int percentComplete = _chromTaskLists.Sum(taskList => taskList == null ? 0 : taskList.PercentComplete) /
_chromTaskLists.Length;
percentComplete = Math.Min(percentComplete, 99);
SetPercentComplete(percentComplete);
return(loaded);
}
//[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);
}
// Disabled 20170131 because Skyline Chorus API is offline
// [TestMethod] TODO(nicksh) re-enable when Chorus is reliable
public void TestThermoDIAChunked()
{
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());
foreach (int chunkChromatogramCount in new[] { 50, 100, 150, 200, 300 })
{
ChromTaskList chromTaskList = new ChromTaskList(() => { }, srmDocument, TEST_ACCOUNT, chorusUrl, ChromTaskList.ChunkChromatogramRequest(chromatogramRequestDocument, chunkChromatogramCount));
chromTaskList.SetMinimumSimultaneousTasks(30);
DateTime startTime = DateTime.Now;
while (chromTaskList.PercentComplete < 100)
{
Thread.Sleep(100);
}
DateTime endTime = DateTime.Now;
AssertEx.AreNoExceptions(chromTaskList.ListExceptions());
Console.Out.WriteLine("*******************************************");
Console.Out.WriteLine("Chromatograms per chunk: {0}", chunkChromatogramCount);
Console.Out.WriteLine("Number of chunks: {0}", chromTaskList.TaskCount);
Console.Out.WriteLine("Elapsed time {0}", endTime.Subtract(startTime));
Console.Out.WriteLine("*******************************************");
}
}
public override bool GetChromatogram(
int id,
string modifiedSequence,
Color peptideColor,
out ChromExtra extra,
out float[] times,
out int[] scanIndexes,
out float[] intensities,
out float[] massErrors)
{
bool loaded = false;
extra = null;
times = null;
scanIndexes = null;
intensities = null;
massErrors = null;
int idRemain = id;
for (int iTaskList = 0; iTaskList < _chromatogramRequestProviders.Length; iTaskList++)
{
ChromatogramRequestProvider requestProvider = _chromatogramRequestProviders[iTaskList];
if (requestProvider.ChromKeys.Count <= idRemain)
{
idRemain -= requestProvider.ChromKeys.Count;
continue;
}
ChromTaskList chromTaskList = _chromTaskLists[iTaskList];
if (null == chromTaskList)
{
chromTaskList = _chromTaskLists[iTaskList] = new ChromTaskList(CheckCancelled, _document, _chorusAccount, requestProvider.ChorusUrl, ChromTaskList.ChunkChromatogramRequest(requestProvider.GetChromatogramRequest(), 1000));
chromTaskList.SetMinimumSimultaneousTasks(3);
}
ChromKey chromKey = requestProvider.ChromKeys[idRemain];
loaded = chromTaskList.GetChromatogram(chromKey, out times, out scanIndexes, out intensities, out massErrors);
if (loaded)
{
extra = new ChromExtra(id, chromKey.Precursor == 0 ? 0 : -1);
if (times.Length > 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
extra.StatusId,
extra.StatusRank,
times,
intensities);
}
}
break;
}
int percentComplete = _chromTaskLists.Sum(taskList => taskList == null ? 0 : taskList.PercentComplete) /
_chromTaskLists.Length;
percentComplete = Math.Min(percentComplete, 99);
SetPercentComplete(percentComplete);
return(loaded);
}
