public TaskItem(Workspace workspace, DbLock dbLock)
{
Workspace = workspace;
DbLock = dbLock;
}
public ChromatogramTask(Workspace workspace, DbLock dbLock)
: base(workspace, dbLock)
{
}
public ResultCalculatorTask(PeptideAnalysis peptideAnalysis, DbLock dbLock)
: base(peptideAnalysis.Workspace, dbLock)
{
PeptideAnalysis = peptideAnalysis;
}
private ChromatogramTask GetTaskList()
{
long? msDataFileId = null;
var analysisChromatograms = new List<AnalysisChromatograms>();
bool openAnalyses = false;
string dataFilePath = null;
if (string.IsNullOrEmpty(_workspace.GetDataDirectory()))
{
return null;
}
var workspaceCopy = _workspace.Clone();
foreach (var peptideAnalysis in workspaceCopy.PeptideAnalyses)
{
if (0 == peptideAnalysis.GetChromatogramRefCount() || !peptideAnalysis.ChromatogramsWereLoaded)
{
continue;
}
foreach (var peptideFileAnalysis in peptideAnalysis.FileAnalyses)
{
if (_workspace.IsRejected(peptideFileAnalysis.MsDataFile))
{
continue;
}
if (!peptideFileAnalysis.PeptideAnalysis.ChromatogramsWereLoaded)
{
continue;
}
if (peptideFileAnalysis.ChromatogramSet == null || !peptideFileAnalysis.IsMzKeySetComplete(peptideFileAnalysis.ChromatogramSet.Chromatograms.Keys))
{
if (msDataFileId == null)
{
dataFilePath = _workspace.GetDataFilePath(peptideFileAnalysis.MsDataFile.Name);
if (dataFilePath == null)
{
continue;
}
msDataFileId = peptideFileAnalysis.MsDataFile.Id;
openAnalyses = true;
}
else
{
if (!Equals(msDataFileId, peptideFileAnalysis.MsDataFile.Id))
{
continue;
}
}
analysisChromatograms.Add(new AnalysisChromatograms(peptideFileAnalysis));
}
}
}
int missingChromatograms = 0;
if (!openAnalyses)
{
if (!_workspace.SavedWorkspaceChange.HasChromatogramMassChange)
{
ICollection<long> lockedMsDataFileIds;
using (_session = _workspace.OpenSession())
{
lockedMsDataFileIds = ListLockedMsDataFileIds(_session);
}
foreach (var peptideAnalysis in workspaceCopy.PeptideAnalyses)
{
foreach (var fileAnalysis in peptideAnalysis.FileAnalyses)
{
if (fileAnalysis.ChromatogramSetId != null)
{
continue;
}
missingChromatograms++;
if (lockedMsDataFileIds.Contains(fileAnalysis.MsDataFile.Id))
{
continue;
}
if (_workspace.IsRejected(fileAnalysis.MsDataFile))
{
continue;
}
if (null == msDataFileId)
{
msDataFileId = fileAnalysis.MsDataFile.Id;
}
else
{
if (msDataFileId != fileAnalysis.MsDataFile.Id)
{
continue;
}
}
analysisChromatograms.Add(new AnalysisChromatograms(fileAnalysis));
}
}
}
}
_missingChromatograms = missingChromatograms;
if (!msDataFileId.HasValue)
{
return null;
}
DbLock dbLock = null;
var msDataFile = _workspace.MsDataFiles.FindByKey(msDataFileId.Value);
if (!openAnalyses)
{
dbLock = new DbLock
{
InstanceIdGuid = _workspace.InstanceId,
MsDataFileId = msDataFileId,
LockType = LockType.chromatograms
};
}
return new ChromatogramTask(workspaceCopy, dbLock)
{
AnalysisChromatograms = analysisChromatograms,
MsDataFile = msDataFile,
DataFilePath = dataFilePath,
};
}
private ResultCalculatorTask GetNextPeptideAnalysis()
{
if (!_workspace.IsLoaded)
{
StatusMessage = "Waiting for workspace to load";
return null;
}
StatusMessage = "Polling for database changes";
_workspace.DatabasePoller.MergeChangesNow();
StatusMessage = "Looking for next peptide";
var workspaceClone = _workspace.Clone();
var peptideAnalyses = workspaceClone.PeptideAnalyses;
var openPeptideAnalysisIds = new HashSet<long>();
foreach (var peptideAnalysis in peptideAnalyses.Where(pa=>0 != pa.GetChromatogramRefCount()))
{
openPeptideAnalysisIds.Add(peptideAnalysis.Id);
if (peptideAnalysis.FileAnalyses.Count == 0)
{
continue;
}
foreach (var peptideFileAnalysis in peptideAnalysis.FileAnalyses)
{
if (peptideFileAnalysis.ValidationStatus == ValidationStatus.reject)
{
continue;
}
if (peptideFileAnalysis.ChromatogramSet == null)
{
continue;
}
if (peptideFileAnalysis.CalculatedPeaks != null)
{
continue;
}
return new ResultCalculatorTask(peptideAnalysis, null);
}
}
if (workspaceClone.SavedWorkspaceChange.HasTurnoverChange)
{
return null;
}
_pendingAnalysisCount =
peptideAnalyses.Count(
pa =>
0 == pa.GetChromatogramRefCount() &&
pa.FileAnalyses.Any(fa => !fa.PeakData.IsCalculated && fa.ChromatogramSetId.HasValue));
var lockedIds = ListLockedAnalyses();
foreach (var peptideAnalysis in peptideAnalyses)
{
if (lockedIds.Contains(peptideAnalysis.Id))
{
continue;
}
if (peptideAnalysis.GetChromatogramRefCount() > 0)
{
continue;
}
var uncalculatedCount = peptideAnalysis.FileAnalyses.Count(entry =>
!entry.PeakData.IsCalculated &&
entry.ChromatogramSetId.HasValue);
if (uncalculatedCount > 0)
{
peptideAnalysis.IncChromatogramRefCount();
var workspaceData = _workspace.DatabasePoller.LoadChanges(workspaceClone.Data, new Dictionary<long, bool>
{
{peptideAnalysis.Id, true}
});
workspaceClone.Merge(workspaceData);
if (!IsRunning())
{
return null;
}
DbLock dbLock;
using (_session = _workspace.OpenWriteSession())
{
try
{
_session.BeginTransaction();
dbLock = new DbLock
{
InstanceIdGuid = _workspace.InstanceId,
LockType = LockType.results,
PeptideAnalysisId = peptideAnalysis.Id
};
_session.Save(dbLock);
_session.Transaction.Commit();
}
catch (HibernateException hibernateException)
{
throw new LockException("Could not insert lock", hibernateException);
}
}
return new ResultCalculatorTask(peptideAnalysis, dbLock);
}
}
return null;
}
