public void Start()
{
lock (this)
{
if (_started)
{
return;
}
_started = true;
}
Task.Factory.StartNew(() =>
{
try
{
SendRequest();
}
finally
{
lock (this)
{
_finished = true;
ChromTaskList.OnTaskCompleted(this);
}
}
});
}
private void SendRequest()
{
while (true)
{
try
{
var chromatogramCache = ChorusSession.GenerateChromatograms(ChorusAccount, ChorusUrl, ChromatogramRequestDocument);
if (null == chromatogramCache)
{
return;
}
var chromKeyIndiceses = chromatogramCache.GetChromKeys(ChorusUrl).ToList();
lock (this)
{
_chromatogramCache = chromatogramCache;
_chromKeyIndiceses = chromKeyIndiceses;
}
return;
}
catch (Exception exception)
{
ChromTaskList.HandleException(exception);
return;
}
}
}
//[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);
}
public ChromatogramGeneratorTask(ChromTaskList chromTaskList, ChorusAccount chorusAccount, ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
ChromTaskList = chromTaskList;
ChorusAccount = chorusAccount;
ChorusUrl = chorusUrl;
ChromatogramRequestDocument = chromatogramRequestDocument;
}
public ChromatogramGeneratorTask(ChromTaskList chromTaskList, ChorusAccount chorusAccount, ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
ChromTaskList = chromTaskList;
ChorusAccount = chorusAccount;
ChorusUrl = chorusUrl;
ChromatogramRequestDocument = chromatogramRequestDocument;
}
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;
Assert.AreEqual(0, chromTaskList.ListExceptions().Count);
Console.Out.WriteLine("Elapsed time {0}", endTime.Subtract(startTime));
}
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;
}
