public static MidasLibrary Create(LibrarySpec libSpec)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(libSpec.FilePath, typeof(MidasLibrary), true))
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), true))
using (var transaction = session.BeginTransaction())
{
session.Save(new DbLibInfo {
SchemaVersion = SCHEMA_VERSION_CURRENT, Guid = Guid.NewGuid().ToString()
});
transaction.Commit();
return(new MidasLibrary(libSpec));
}
}
public static void SaveSnack(SnackViewModel snackViewModel)
{
var sessionFactory = SessionFactoryFactory.GetFactory();
using (var session = sessionFactory.OpenSession())
{
using (var trans = session.BeginTransaction())
{
var snackModel = SnackMap.VmToModel(snackViewModel);
session.SaveOrUpdate(snackModel);
trans.Commit();
}
}
}
public static IEnumerable <SnackViewModel> GetSnacks()
{
var sessionFactory = SessionFactoryFactory.GetFactory();
using (var session = sessionFactory.OpenSession())
{
using (var trans = session.BeginTransaction())
{
var snackVMs = session.CreateCriteria <Snack>().List <Snack>();
return(snackVMs.Select(SnackMap.ModelToVm));
}
}
}
public static ProteomeDb CreateProteomeDb(String path)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(path, TYPE_DB, true))
{
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), true))
using (var transaction = session.BeginTransaction())
{
session.Save(new DbVersionInfo {
SchemaVersionMajor = SCHEMA_VERSION_MAJOR_CURRENT, SchemaVersionMinor = SCHEMA_VERSION_MINOR_CURRENT
});
transaction.Commit();
}
}
return(OpenProteomeDb(path));
}
public static IrtDb CreateIrtDb(string path)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(path, typeof(IrtDb), true))
{
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), true))
using (var transaction = session.BeginTransaction())
{
session.Save(new DbVersionInfo {
SchemaVersion = SCHEMA_VERSION_CURRENT
});
transaction.Commit();
}
}
return(GetIrtDb(path, null));
}
protected override IDisposable Connect()
{
DbProviderFactory fact = new SQLiteFactory();
SQLiteConnection conn = (SQLiteConnection)fact.CreateConnection();
if (conn != null)
{
var connectionStringBuilder =
SessionFactoryFactory.SQLiteConnectionStringBuilderFromFilePath(FilePath);
connectionStringBuilder.Version = 3;
conn.ConnectionString = connectionStringBuilder.ToString();
conn.Open();
}
return(conn);
}
private void OpenSessionFactory()
{
if (!ReferenceEquals(this, _owner))
{
return;
}
if (SessionFactory != null)
{
throw new InvalidOperationException("SessionFactory is already open");
}
if (Path.GetExtension(DatabasePath) == TpgLinkDef.Extension)
{
_tpgLinkDef = TpgLinkDef.Load(DatabasePath);
_sessionFactory = SessionFactoryFactory.CreateSessionFactory(TpgLinkDef, 0);
}
else
{
_sessionFactory = SessionFactoryFactory.CreateSessionFactory(DatabasePath, 0);
}
}
public void RemoveResultsFiles(params string[] resultsFiles)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(FilePath, typeof(MidasLibrary), false))
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), true))
using (var transaction = session.BeginTransaction())
{
foreach (var kvp in _spectra)
{
if (resultsFiles.Contains(kvp.Key.FilePath))
{
foreach (var spectrum in kvp.Value)
{
session.Delete(spectrum);
}
session.Delete(kvp.Key);
}
}
transaction.Commit();
}
}
void testModelFile(TestModel testModel, string filename)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(filename))
using (var session = testModel.session = sessionFactory.OpenSession())
{
Assert.AreEqual(SchemaUpdater.CurrentSchemaRevision, session.UniqueResult <int>("SELECT SchemaRevision FROM About"));
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources();
testModel.TestSpectra();
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
}
}
public static void ComputeData(Stopwatch sw)
{
sw.Restart();
var sessFactFactory = new SessionFactoryFactory(false);
var sessionFactory = sessFactFactory.GetSessionFactory();
var repository = new Repository(sessionFactory);
repository.Clear();
AggregationServices services = new AggregationServices(repository);
services.ReAggregateAllOperations();
sw.Stop();
Console.WriteLine("Profiles computed in: {0}", sw.ElapsedMilliseconds);
sw.Restart();
services.ComputeBalancesForAllAccounts();
repository.Flush();
sw.Stop();
Console.WriteLine("Balances computed in: {0}", sw.ElapsedMilliseconds);
}
public ISessionFactory CreateDatabase()
{
using (var connection = OpenConnection(GetConnectionStringNoDatabase()))
{
var cmd = connection.CreateCommand();
cmd.CommandText = "CREATE DATABASE " + Database;
cmd.ExecuteNonQuery();
}
using (var connection = OpenConnection(GetConnectionString()))
{
if (DatabaseTypeEnum == DatabaseTypeEnum.mysql)
{
var cmd = connection.CreateCommand();
cmd.CommandText = "SET storage_engine=INNODB";
cmd.ExecuteNonQuery();
}
var configuration = SessionFactoryFactory.GetConfiguration(DatabaseTypeEnum, 0);
var schemaExport = new SchemaExport(configuration);
schemaExport.Execute(false, true, false, connection, null);
}
return(SessionFactoryFactory.CreateSessionFactory(this, SessionFactoryFlags.CreateSchema));
}
protected Workspace CreateWorkspace(string path, DbTracerDef dbTracerDef)
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(path, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
var transaction = session.BeginTransaction();
var dbWorkspace = new DbWorkspace
{
ModificationCount = 1,
TracerDefCount = dbTracerDef == null ? 0 : 1,
SchemaVersion = WorkspaceUpgrader.CurrentVersion,
};
session.Save(dbWorkspace);
if (dbTracerDef != null)
{
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
}
var modification = new DbModification
{
DeltaMass = 57.021461,
Symbol = "C",
Workspace = dbWorkspace
};
session.Save(modification);
transaction.Commit();
}
}
var workspace = new Workspace(path);
workspace.SetTaskScheduler(TaskScheduler.Default);
workspace.DatabasePoller.LoadAndMergeChanges(null);
return(workspace);
}
public static ISessionFactory CreateSessionFactory(String path, bool createSchema)
{
return(SessionFactoryFactory.CreateSessionFactory(path, typeof(BlibDb), createSchema));
}
public ISessionFactory OpenSessionFactory()
{
return(SessionFactoryFactory.CreateSessionFactory(this, 0));
}
public void TestSchemaUpdater()
{
Assert.AreEqual(15, SchemaUpdater.CurrentSchemaRevision);
var testModel = new TestModel()
{
TestContext = TestContext
};
TestModel.ClassInitialize(TestContext);
testModel.TestInitialize();
testModelFile(testModel, "testModel.idpDB");
string filename = null;
// test all revisions without a data filter applied
// we don't need to test upgrade from 12 to 13; the extra table (PeptideModificationProbability) is ignored and necessary for the current NHibernate bindings
// we don't need to test upgrade from 11 to 12; the changed table (XICMetrics) is ignored
// we don't need to test upgrade from 10 to 11; the extra columns (GeneGroups, Genes) are ignored
// we don't need to test upgrade from 9 to 10; the extra tables (XICMetrics, XICMetricsSettings) are ignored
// we don't need to test upgrade from 8 to 9; the extra columns (GeneLevelFiltering, DistinctMatchFormat) are ignored
// we don't need to test upgrade from 7 to 8; the extra columns are ignored
// we don't need to test upgrade from 5 to 6; it simply forces reapplication of the basic filters
// we don't need to test upgrade from 4 to 5; it's a simple null value fix
filename = "testModel-v4.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 4);
testModelFile(testModel, filename);
filename = "testModel-v3.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 3);
testModelFile(testModel, filename);
filename = "testModel-v2.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 2);
testModelFile(testModel, filename);
filename = "testModel-v1.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 1);
testModelFile(testModel, filename);
filename = "testModel-v0.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 0);
testModelFile(testModel, filename);
// test all revisions with a data filter applied (only check that the update worked this time)
File.Copy("testModel.idpDB", "testFilter.idpDB", true);
var dataFilter = new DataFilter {
MaximumQValue = 1
};
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testFilter.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
dataFilter.ApplyBasicFilters(session);
}
filename = "testFilter-v4.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 4);
testFilterFile(filename);
filename = "testFilter-v3.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 3);
testFilterFile(filename);
filename = "testFilter-v2.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 2);
testFilterFile(filename);
filename = "testFilter-v1.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 1);
testFilterFile(filename);
filename = "testFilter-v0.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 0);
testFilterFile(filename);
}
public void TestSchemaUpdater()
{
Assert.AreEqual(18, SchemaUpdater.CurrentSchemaRevision);
var testModel = new TestModel()
{
TestContext = TestContext
};
TestModel.ClassInitialize(TestContext);
testModel.TestInitialize();
testModelFile(testModel, "testModel.idpDB");
string filename = null;
// test all revisions without a data filter applied
// we don't need to test upgrade from 5 to 6; it simply forces reapplication of the basic filters
// we don't need to test upgrade from 4 to 5; it's a simple null value fix
filename = "testModel-v4.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 4);
testModelFile(testModel, filename);
filename = "testModel-v3.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 3);
testModelFile(testModel, filename);
filename = "testModel-v2.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 2);
testModelFile(testModel, filename);
filename = "testModel-v1.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 1);
testModelFile(testModel, filename);
filename = "testModel-v0.idpDB";
File.Copy("testModel.idpDB", filename, true);
downgradeToRevision(filename, 0);
testModelFile(testModel, filename);
// test all revisions with a data filter applied (only check that the update worked this time)
File.Copy("testModel.idpDB", "testFilter.idpDB", true);
var dataFilter = new DataFilter {
MaximumQValue = 1
};
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testFilter.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
dataFilter.ApplyBasicFilters(session);
}
filename = "testFilter-v4.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 4);
testFilterFile(filename);
filename = "testFilter-v3.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 3);
testFilterFile(filename);
filename = "testFilter-v2.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 2);
testFilterFile(filename);
filename = "testFilter-v1.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 1);
testFilterFile(filename);
filename = "testFilter-v0.idpDB";
File.Copy("testFilter.idpDB", filename, true);
downgradeToRevision(filename, 0);
testFilterFile(filename);
}
public static void AddSpectra(MidasLibSpec libSpec, MsDataFilePath[] resultsFiles, SrmDocument doc, ILoadMonitor monitor, out List <MsDataFilePath> failedFiles)
{
// Get spectra from results files
var newSpectra = new List <DbSpectrum>();
var progress = new ProgressStatus(string.Empty).ChangeMessage(Resources.MidasLibrary_AddSpectra_Reading_MIDAS_spectra);
const int percentResultsFiles = 80;
failedFiles = new List <MsDataFilePath>();
for (var i = 0; i < resultsFiles.Length; i++)
{
var resultsFile = resultsFiles[i];
try
{
monitor.UpdateProgress(progress.ChangePercentComplete(i * percentResultsFiles / resultsFiles.Length));
var filePath = resultsFile.GetFilePath();
if (File.Exists(filePath))
{
var sampleIndex = resultsFile.GetSampleIndex();
using (var msd = new MsDataFileImpl(filePath, sampleIndex == -1 ? 0 : sampleIndex, resultsFile.GetLockMassParameters(), requireVendorCentroidedMS2: true))
{
if (ChromatogramDataProvider.HasChromatogramData(msd) && SpectraChromDataProvider.HasSpectrumData(msd))
{
var chromPrecursors = ReadChromPrecursorsFromMsd(msd, monitor).ToList();
newSpectra.AddRange(ReadDbSpectraFromMsd(msd, monitor));
MatchSpectraToChrom(newSpectra, chromPrecursors, monitor);
}
}
MatchSpectraToPeptides(newSpectra, doc, monitor);
}
else
{
failedFiles.Add(resultsFile);
}
}
catch (Exception x)
{
monitor.UpdateProgress(progress.ChangeErrorException(x));
failedFiles.Add(resultsFile);
}
if (monitor.IsCanceled)
{
monitor.UpdateProgress(progress.Cancel());
return;
}
}
if (!newSpectra.Any())
{
monitor.UpdateProgress(progress.Complete());
return;
}
progress = progress.ChangePercentComplete(percentResultsFiles);
monitor.UpdateProgress(progress);
// Add spectra to library
var midasLib = !File.Exists(libSpec.FilePath) ? Create(libSpec) : Load(libSpec, monitor);
if (midasLib == null)
{
monitor.UpdateProgress(progress.ChangeErrorException(new Exception(Resources.MidasLibrary_AddSpectra_Error_loading_MIDAS_library_for_adding_spectra_)));
return;
}
progress = progress.ChangeMessage(Resources.MidasLibrary_AddSpectra_Adding_spectra_to_MIDAS_library);
monitor.UpdateProgress(progress);
var results = new Dictionary <string, DbResultsFile>();
if (midasLib._spectra != null)
{
foreach (var kvp in midasLib._spectra)
{
results[kvp.Key.FilePath] = kvp.Key;
}
}
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(libSpec.FilePath, typeof(MidasLibrary), false))
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), true))
using (var transaction = session.BeginTransaction())
{
for (var i = 0; i < newSpectra.Count; i++)
{
if (monitor.IsCanceled)
{
transaction.Rollback();
monitor.UpdateProgress(progress.Cancel());
return;
}
var spectrum = newSpectra[i];
monitor.UpdateProgress(progress.ChangePercentComplete(percentResultsFiles + (int)(100.0 * i / newSpectra.Count)));
DbResultsFile resultsFile;
if (!results.TryGetValue(spectrum.ResultsFile.FilePath, out resultsFile))
{
resultsFile = new DbResultsFile(spectrum.ResultsFile)
{
Id = null
};
results[spectrum.ResultsFile.FilePath] = resultsFile;
session.SaveOrUpdate(resultsFile);
}
else if (midasLib._spectra != null)
{
List <DbSpectrum> existingSpectra;
if (midasLib._spectra.TryGetValue(resultsFile, out existingSpectra) &&
existingSpectra.Any(x => Equals(x.ResultsFile.FilePath, spectrum.ResultsFile.FilePath) &&
Equals(x.PrecursorMz, spectrum.PrecursorMz) &&
Equals(x.RetentionTime, spectrum.RetentionTime)))
{
// This spectrum already exists in the library
continue;
}
}
var spectrumNewDisconnected = new DbSpectrum(spectrum)
{
Id = null, ResultsFile = resultsFile
};
session.SaveOrUpdate(spectrumNewDisconnected);
}
transaction.Commit();
monitor.UpdateProgress(progress.Complete());
}
}
public void TestInitialize()
{
var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testQueryReader.idpDB", false, false);
session = sessionFactory.OpenSession();
}
private bool Load(IProgressMonitor monitor)
{
_spectra = null;
if (FilePath == null)
{
return(false);
}
var info = new FileInfo(FilePath);
if (!info.Exists || info.Length == 0)
{
return(false);
}
var progress = new ProgressStatus(string.Empty).ChangeMessage(Resources.MidasLibrary_Load_Loading_MIDAS_library);
monitor.UpdateProgress(progress);
var spectra = new Dictionary <DbResultsFile, List <DbSpectrum> >();
try
{
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(FilePath, typeof(MidasLibrary), false))
using (var session = new SessionWithLock(sessionFactory.OpenSession(), new ReaderWriterLock(), false))
{
var libInfo = session.CreateCriteria(typeof(DbLibInfo)).List <DbLibInfo>();
if (libInfo.Count != 1)
{
throw new Exception(Resources.MidasLibrary_Load_Error_reading_LibInfo_from_MIDAS_library);
}
SchemaVersion = libInfo[0].SchemaVersion;
LibraryGuid = libInfo[0].Guid;
var readSpectra = session.CreateCriteria(typeof(DbSpectrum)).List <DbSpectrum>();
progress = progress.ChangeSegments(0, readSpectra.Count);
foreach (var spectrum in readSpectra)
{
if (monitor.IsCanceled)
{
monitor.UpdateProgress(progress.Cancel());
return(false);
}
progress = progress.NextSegment();
monitor.UpdateProgress(progress);
List <DbSpectrum> list;
if (!spectra.TryGetValue(spectrum.ResultsFile, out list))
{
list = new List <DbSpectrum>();
spectra[spectrum.ResultsFile] = list;
}
list.Add(spectrum);
}
}
}
catch
{
monitor.UpdateProgress(progress.Cancel());
return(false);
}
_spectra = spectra;
monitor.UpdateProgress(progress.Complete());
return(true);
}
public void TestChromatogramGenerator()
{
String dbPath = Path.Combine(TestContext.TestDir, "test" + Guid.NewGuid() + ".tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetN15Enrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
var dbMsDataFile = new DbMsDataFile
{
Name = "20090724_HT3_0",
};
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
Assert.IsTrue(MsDataFileUtil.InitMsDataFile(workspace, msDataFile));
DbPeptide dbPeptide;
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
dbPeptide = new DbPeptide
{
Protein = "TestProtein",
Sequence = "YLAAYLLLVQGGNAAPSAADIK",
FullSequence = "K.YLAAYLLLVQGGNAAPSAADIK.A",
};
session.Save(dbPeptide);
var searchResult = new DbPeptideSpectrumMatch
{
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
PrecursorCharge = 3,
RetentionTime = 20.557 * 60,
};
session.Save(searchResult);
session.Transaction.Commit();
}
var peptide = new Peptide(workspace, dbPeptide);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
peptideAnalysis.IncChromatogramRefCount();
var peptideFileAnalysis = PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
workspace.DatabasePoller.LoadAndMergeChanges(null);
peptideAnalysis.IncChromatogramRefCount();
var chromatogramGenerator = new ChromatogramGenerator(workspace);
chromatogramGenerator.Start();
while (peptideFileAnalysis.ChromatogramSet == null)
{
Thread.Sleep(100);
}
var chromatogramDatas = peptideFileAnalysis.GetChromatograms();
Assert.IsFalse(chromatogramDatas.Chromatograms.Count == 0);
chromatogramGenerator.Stop();
while (chromatogramGenerator.IsThreadAlive)
{
Thread.Sleep(100);
}
}
public void TestImportExportIdpXml()
{
var testModel = new TestModel();
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testModel.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
var distinctAnalyses = testModel.session.Query <Analysis>();
foreach (var analysis in distinctAnalyses)
{
session.Save(new AnalysisParameter()
{
Analysis = analysis,
Name = "ProteinDatabase",
Value = "testImportExport.fasta"
});
}
/*IList<string> idpXmlPaths;
* using (var exporter = new Exporter(session))
* {
* idpXmlPaths = exporter.WriteIdpXml(true, true);
* exporter.WriteSpectra();
* exporter.WriteProteins("testImportExport.fasta", false);
* }*/
session.Close();
/*using (var parser = new Parser(".", qonverterSettingsHandler, false, idpXmlPaths.ToArray()))
* {
* // ReadXml should pick up mzML files in the same directory as the idpXMLs
* parser.Start();
* }*/
//var merger = new Merger("testImportExport.idpDB", idpXmlPaths.Select(o => Path.ChangeExtension(o, ".idpDB")));
//merger.Start();
}
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testImportExport.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
foreach (var analysis in session.Query <Analysis>())
{
session.Delete(session.UniqueResult <AnalysisParameter>(o => o.Analysis.Id == analysis.Id &&
o.Name == "ProteinDatabase"));
}
session.Flush();
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources();
testModel.TestSpectra();
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
// TODO: enable QonverterSettings round trip for idpXML?
//testModel.TestQonverterSettings();
}
}
// TODO(nicksh): 2013-10-03: Re-enable this test once it reliably passes
//[TestMethod]
public void TestPeakFinder()
{
String dbPath = Path.Combine(TestContext.TestDir, "PeakFinderTest.tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
SettingCount = 2,
SchemaVersion = WorkspaceUpgrader.CurrentVersion
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetD3LeuEnrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.mass_accuracy.ToString(),
Value = "100000"
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
workspace.DatabasePoller.LoadAndMergeChanges(null);
foreach (var peakFinderPeptide in peptides)
{
AddPeptide(workspace, peakFinderPeptide);
}
while (true)
{
string statusMessage;
int progress;
workspace.ChromatogramGenerator.GetProgress(out statusMessage, out progress);
if ("Idle" == statusMessage)
{
break;
}
Thread.Sleep(100);
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var exceptions = new List <Exception>();
foreach (var peptide in peptides)
{
try
{
TestPeptide(workspace, peptide);
}
catch (Exception exception)
{
exceptions.Add(exception);
Trace.TraceError("{0}:{1}", peptide.PeptideSequence, exception);
}
}
CollectionAssert.AreEqual(new Exception[0], exceptions);
}
public void TestStaticQonverter()
{
#region Example with forward and reverse proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEK",
"TIDERPEPTIDEKPEP",
"DERPEPTIDEKPEPTI",
"THEQUICKBRWNFXUMPSVERTHELZYDG",
"KEDITPEPREDITPEP",
"PEPKEDITPEPREDIT",
"ITPEPKEDITPEPRED",
"GDYZLEHTREVSPMUXFNWRBKCIUQEHT"
};
const string decoyPrefix = "r-";
const int analysisCount = 2;
const int sourceCount = 2;
const int chargeCount = 2;
File.Delete("testStaticQonversion.idpDB");
var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testStaticQonversion.idpDB", new SessionFactoryConfig {
CreateSchema = true
});
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
session.Clear();
// add decoy prefix to the second half of the proteins
for (long i = testProteinSequences.LongLength / 2; i < testProteinSequences.LongLength; ++i)
{
var pro = session.Get <Protein>(i + 1);
pro.Accession = decoyPrefix + pro.Accession;
session.Update(pro);
}
#endregion
#region Example PSMs
// For each combination of 2 engines, 2 sources, and 2 charges,
// we test qonversion on this scenario:
//
// Scan Score DecoyState Targets Decoys Ambiguous -> Expected QValue
// 50 6 T 1 0 0 0
// 30 5 T 2 0 0 0
// 40 4 T 3 0 0 0
// 10 3 D 3 1 0 2/4
// 20 2 D 3 2 0 4/5
// 60 1 T 4 2 0 4/6
double q = PeptideSpectrumMatch.DefaultQValue;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
{
for (int source = 1; source <= sourceCount; ++source)
{
for (int charge = 1; charge <= chargeCount; ++charge)
{
List <SpectrumTuple> testPsmSummary = new List <SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/", source, 5, analysis, 6, q, String.Format("TIDERPEPTIDEK@{0}/1 PEPTIDER@{0}/8", charge)),
new SpectrumTuple("/", source, 3, analysis, 5, q, String.Format("TIDERPEPTIDEK@{0}/1 PEPTIDER@{0}/2", charge)),
new SpectrumTuple("/", source, 4, analysis, 4, q, String.Format("EDITPEP@{0}/1 THEQUICKBR@{0}/4", charge)),
new SpectrumTuple("/", source, 1, analysis, 3, q, String.Format("PEPTIDEKPEP@{0}/1 PEPTIDEK@{0}/2", charge)),
new SpectrumTuple("/", source, 2, analysis, 2, q, String.Format("TIDER@{0}/1 PEPTIDER@{0}/2", charge)),
new SpectrumTuple("/", source, 6, analysis, 1, q, String.Format("EDITPEPR@{0}/1 TIDERPEPTIDEK@{0}/3", charge))
};
TestModel.CreateTestData(session, testPsmSummary);
}
}
}
List <SpectrumTuple> testPsmSummaryWithoutScores = new List <SpectrumTuple>()
{
new SpectrumTuple("/", 1, 1, analysisCount + 1, null, 0.01, "TIDERPEPTIDEK@1/1 PEPTIDER@3/8"),
new SpectrumTuple("/", 1, 2, analysisCount + 1, null, 0.02, "KEDITPEPR@2/1 PEPTIDEK@2/8"),
new SpectrumTuple("/", 1, 3, analysisCount + 1, null, 0.03, "THEQUICKBR@3/1 THELZYDG@1/8"),
};
TestModel.CreateTestData(session, testPsmSummaryWithoutScores);
// force all peptide instances to fully specific
foreach (PeptideInstance pi in session.Query <PeptideInstance>())
{
pi.NTerminusIsSpecific = pi.CTerminusIsSpecific = true;
session.Update(pi);
}
session.Flush();
session.Close(); // close the connection
sessionFactory.Close();
#endregion
var qonverter = new IDPicker.Qonverter()
{
SettingsByAnalysis = new Dictionary <int, Qonverter.Settings>()
};
for (int i = 1; i <= analysisCount + 1; ++i)
{
qonverter.SettingsByAnalysis[i] = new Qonverter.Settings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
ChargeStateHandling = Qonverter.ChargeStateHandling.Ignore,
TerminalSpecificityHandling = Qonverter.TerminalSpecificityHandling.Ignore,
MassErrorHandling = Qonverter.MassErrorHandling.Ignore,
MissedCleavagesHandling = Qonverter.MissedCleavagesHandling.Ignore,
DecoyPrefix = decoyPrefix,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1
} },
{ "score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 0
} }
}
}
}
;
var progressTester = new QonversionProgressTest()
{
Qonverter = qonverter,
ExpectedTotalAnalyses = analysisCount * sourceCount // engine 3 is ignored
};
File.Copy("testStaticQonversion.idpDB", "testStaticQonversion2.idpDB", true);
// test without progress monitor
qonverter.Qonvert("testStaticQonversion2.idpDB");
qonverter.QonversionProgress += new IDPicker.Qonverter.QonversionProgressEventHandler(progressTester.qonverter_QonversionProgress);
File.Copy("testStaticQonversion.idpDB", "testStaticQonversion3.idpDB", true);
// test progress monitor with cancelling
// (must before a full qonversion since the QValue test doesn't expect cancellation)
progressTester.ExpectedQonvertedAnalyses = 0;
progressTester.CancelAtCount = 4;
qonverter.Qonvert("testStaticQonversion3.idpDB");
// test progress monitor without cancelling
progressTester.ExpectedQonvertedAnalyses = 0;
progressTester.CancelAtCount = int.MaxValue;
qonverter.Qonvert("testStaticQonversion.idpDB");
sessionFactory = SessionFactoryFactory.CreateSessionFactory("testStaticQonversion.idpDB");
session = sessionFactory.OpenSession();
session.Clear();
#region QValue test
Dictionary <long, double> expectedQValues = new Dictionary <long, double>()
{
// with high scoring decoys, Q values can spike and gradually go down again;
// we squash these spikes such that Q value is monotonically increasing;
// then we convert Q values to FDR scores using linear interpolation
// targets decoys ambiguous unadjusted-Q-value adjusted-Q-value FDR-score
{ 4, 0 }, // 1 0 0 0 0 0
{ 2, 0.2 }, // 2 0 0 0 0 0.2
{ 3, 0.4 }, // 2 1 0 0.666 0.4 0.4
{ 0, 0.488 }, // 3 1 0 0.5 0.4 0.488
{ 1, 0.577 }, // 4 1 0 0.4 0.4 0.577
{ 5, 0.666 }, // 4 2 0 0.666 0.666 0.666
};
for (long engine = 1; engine <= 2; ++engine)
{
for (long source = 1; source <= 2; ++source)
{
for (int charge = 1; charge <= 2; ++charge)
{
foreach (var itr in expectedQValues)
{
var topRankedMatch = session.CreateQuery("SELECT psm " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Analysis.id = ? " +
" AND psm.Spectrum.Source.id = ? " +
" AND psm.Spectrum.Index = ? " +
" AND psm.Charge = ? " +
" AND psm.Rank = 1" +
"GROUP BY psm.Spectrum.id ")
.SetParameter(0, engine)
.SetParameter(1, source)
.SetParameter(2, itr.Key)
.SetParameter(3, charge)
.List <PeptideSpectrumMatch>().First();
Assert.AreEqual(session.Get <Analysis>(engine), topRankedMatch.Analysis);
Assert.AreEqual(session.Get <SpectrumSource>(source), topRankedMatch.Spectrum.Source);
Assert.AreEqual(charge, topRankedMatch.Charge);
Assert.AreEqual(itr.Value, topRankedMatch.QValue, 1e-3);
}
}
}
}
var scorelessMatches = session.CreateQuery("SELECT psm " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Analysis.id = 3 " +
" AND psm.Rank = 1")
.List <PeptideSpectrumMatch>();
Assert.AreEqual(3, scorelessMatches.Count);
Assert.AreEqual(0.01, scorelessMatches[0].QValue, 1e-12);
Assert.AreEqual(0.02, scorelessMatches[1].QValue, 1e-12);
Assert.AreEqual(0.03, scorelessMatches[2].QValue, 1e-12);
#endregion
}
public static ISessionFactory CreateSessionFactory_Redundant(String path, bool createSchema)
{
return(SessionFactoryFactory.CreateSessionFactory(path, typeof(BlibDb), @"mapping_redundant.xml", createSchema));
}
/// <summary>
/// Maintains a single string globally for each path, in order to keep from
/// having two threads accessing the same database at the same time.
/// </summary>
private static ISessionFactory GetSessionFactory(string path)
{
return(SessionFactoryFactory.CreateSessionFactory(path, typeof(IrtDb), false));
}
public void TestMergerModel()
{
#region Example proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"RPEPKTIDERPEPKTIDE",
"EDITPEPKEDITPEPR",
"PEPREDITPEPKEDIT",
"EPPIERPETPDETKTDPEPIIRDE"
};
#endregion
#region Example PSMs
List <SpectrumTuple> mergeSourcePsmSummary1 = new List <SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/A/1", 1, 1, 1, 12, 0, "[C2H2O1]PEPTIDE@2/1 TIDERPEPTIDEK@4/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 1, 23, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 1, 34, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 1, 43, 0, "PEPTIDE@2/1 E[H-2O-1]DIT[P1O4]PEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 1, 32, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 1, 21, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 1, 56, 0, "TIDEK@2/1 TIDE@1/2 P[P1O4]EPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 1, 45, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 1, 34, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 1, 65, 0, "TIDERPEPTIDEK@4/1 PETPDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 1, 53, 0, "E[H-2O-1]DITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 1, 42, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 1, 20, 0, "EPPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 1, 24, 0, "PETPDETK@2/1 PEPTIDEK@3/5 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 1, 24, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
List <SpectrumTuple> mergeSourcePsmSummary2 = new List <SpectrumTuple>()
{
new SpectrumTuple("/A/1", 1, 1, 2, 120, 0, "TIDERPEPTIDEK@4/1 PEPTIDE@2/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 2, 230, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 2, 340, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 2, 430, 0, "PEPTIDE@2/1 EDITPEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 2, 320, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 2, 210, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 2, 560, 0, "TIDEK@2/1 TIDE@1/2 PEPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 2, 450, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 2, 340, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 2, 650, 0, "TIDERPEPTIDEK@4/1 PET[P1O4]PDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 2, 530, 0, "EDITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 2, 420, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 2, 200, 0, "E[H-2O-1]PPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 2, 240, 0, "PEPTIDEK@2/1 PETPDETK@2/4 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 2, 240, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
var qonverterSettings1 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
DecoyPrefix = "quiRKy",
RerankMatches = true,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Linear
} },
{ "score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 42,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Quantile
} }
}
};
var qonverterSettings2 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.SVM,
DecoyPrefix = "___---",
RerankMatches = false,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "foo", new Qonverter.Settings.ScoreInfo()
{
Weight = 7,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
} },
{ "bar", new Qonverter.Settings.ScoreInfo()
{
Weight = 11,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
} }
}
};
#endregion
File.Delete("testMergeSource1.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB", new SessionFactoryConfig {
CreateSchema = true
}))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary1);
TestModel.AddSubsetPeakData(session);
qonverterSettings1.Analysis = session.UniqueResult <Analysis>(o => o.Software.Name == "Engine 1");
session.Save(qonverterSettings1);
session.Flush();
}
File.Delete("testMergeSource2.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource2.idpDB", new SessionFactoryConfig {
CreateSchema = true
}))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(session);
// copy is required because session.Save() takes ownership of the instance
var qonverterSettings2Copy = new QonverterSettings()
{
Analysis = session.UniqueResult <Analysis>(o => o.Software.Name == "Engine 2"),
QonverterMethod = qonverterSettings2.QonverterMethod,
DecoyPrefix = qonverterSettings2.DecoyPrefix,
RerankMatches = qonverterSettings2.RerankMatches,
ScoreInfoByName = qonverterSettings2.ScoreInfoByName
};
session.Save(qonverterSettings2Copy);
session.Flush();
}
// create a new merged idpDB from two idpDB files
File.Delete("testMerger.idpDB");
Merger.Merge("testMerger.idpDB", new string[] { "testMergeSource1.idpDB", "testMergeSource2.idpDB" });
var testModel = new TestModel();
// test that testMerger.idpDB passes the TestModel tests
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMerger.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources(false);
testModel.TestSpectra(false);
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
testModel.TestQonverterSettings();
}
// create an in-memory representation of testMergeSource2
var memoryFactory = SessionFactoryFactory.CreateSessionFactory(":memory:", new SessionFactoryConfig {
CreateSchema = true
});
var memoryConnection = SessionFactoryFactory.CreateFile(":memory:");
var memorySession = memoryFactory.OpenSession(memoryConnection);
{
TestModel.CreateTestProteins(memorySession, testProteinSequences);
TestModel.CreateTestData(memorySession, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(memorySession);
qonverterSettings2.Analysis = memorySession.UniqueResult <Analysis>(o => o.Software.Name == "Engine 2");
memorySession.Save(qonverterSettings2);
memorySession.Flush();
}
// merge the in-memory connection into the testMergeSource1 file
/*Merger.Merge("testMergeSource1.idpDB", memoryConnection as System.Data.SQLite.SQLiteConnection);
*
* // testMergeSource1.idpDB should pass just like testMerger.idpDB
* using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB"))
* using (var session = testModel.session = sessionFactory.OpenSession())
* {
* testModel.TestOverallCounts();
* testModel.TestSanity();
* testModel.TestProteins();
* testModel.TestPeptides();
* testModel.TestPeptideInstances();
* testModel.TestSpectrumSourceGroups();
* testModel.TestSpectrumSources(false);
* testModel.TestSpectra(false);
* testModel.TestAnalyses();
* testModel.TestPeptideSpectrumMatches();
* testModel.TestModifications();
* testModel.TestQonverterSettings();
* }*/
}
