public async Task <OperationResultResponse <WorkspaceInfo> > ExecuteAsync(GetWorkspaceFilter filter)
{
DbWorkspace dbWorkspace = await _repository.GetAsync(filter);
if (dbWorkspace is null)
{
return(_responseCreator.CreateFailureResponse <WorkspaceInfo>(HttpStatusCode.NotFound));
}
if (!dbWorkspace.Users.Select(u => u.UserId).Contains(_httpContextAccessor.HttpContext.GetUserId()))
{
return(_responseCreator.CreateFailureResponse <WorkspaceInfo>(HttpStatusCode.Forbidden));
}
OperationResultResponse <WorkspaceInfo> response = new();
List <UserData> usersData = await GetUsersAsync(dbWorkspace.Users?.Select(u => u.UserId).ToList(), response.Errors);
List <ImageInfo> imagesInfo = (await GetImagesAsync(
usersData?.Where(u => u.ImageId.HasValue).Select(u => u.ImageId.Value).ToList(),
response.Errors))
?.Select(_imageMapper.Map).ToList();
response.Status = response.Errors.Any() ? OperationResultStatusType.PartialSuccess : OperationResultStatusType.FullSuccess;
response.Body = _workspaceInfoMapper.Map(
dbWorkspace,
usersData?.Select(u => _userMapper.Map(u, imagesInfo?.FirstOrDefault(i => i.Id == u.ImageId))).ToList());
return(response);
}
public async Task <OperationResultResponse <bool> > ExecuteAsync(Guid workspaceId, JsonPatchDocument <EditWorkspaceRequest> request)
{
DbWorkspace dbWorkspace = await _repository.GetAsync(workspaceId);
Guid editorId = _httpContextAccessor.HttpContext.GetUserId();
if (dbWorkspace.CreatedBy != editorId &&
(await _userRepository.GetAdminsAsync(workspaceId)).FirstOrDefault(wa => wa.UserId == editorId) == null &&
!await _accessValidator.IsAdminAsync())
{
return(_responseCreator.CreateFailureResponse <bool>(HttpStatusCode.Forbidden));
}
if (!_validator.ValidateCustom(request, out List <string> errors))
{
return(_responseCreator.CreateFailureResponse <bool>(HttpStatusCode.BadRequest, errors));
}
OperationResultResponse <bool> response = new();
response.Body = await _repository.EditAsync(dbWorkspace, await _mapper.MapAsync(request));
response.Status = OperationResultStatusType.FullSuccess;
if (!response.Body)
{
response = _responseCreator.CreateFailureResponse <bool>(HttpStatusCode.BadRequest);
}
return(response);
}
public WorkspaceInfo Map(DbWorkspace dbWorkspace, List <UserInfo> users)
{
if (dbWorkspace is null)
{
return(null);
}
ImageConsist image = dbWorkspace.ImageContent is null
? null
: new() { Content = dbWorkspace.ImageContent, Extension = dbWorkspace.ImageExtension };
return(new WorkspaceInfo
{
Id = dbWorkspace.Id,
Name = dbWorkspace.Name,
Description = dbWorkspace.Description,
Image = image,
CreatedAtUtc = dbWorkspace.CreatedAtUtc,
CreatedBy = users?.FirstOrDefault(u => u.Id == dbWorkspace.CreatedBy),
IsActive = dbWorkspace.IsActive,
Channels = dbWorkspace.Channels?
.Select(_channelInfoMapper.Map).ToList(),
Users = users?
.Where(u => dbWorkspace.Users.Any(wu => wu.UserId == u.Id)).ToList()
});
}
}
public async Task <Guid?> CreateAsync(DbWorkspace dbWorkspace)
{
if (dbWorkspace is null)
{
return(null);
}
_provider.Workspaces.Add(dbWorkspace);
await _provider.SaveAsync();
return(dbWorkspace.Id);
}
public async Task <bool> EditAsync(DbWorkspace dbWorkspace, JsonPatchDocument <DbWorkspace> request)
{
if (dbWorkspace is null || request is null)
{
return(false);
}
request.ApplyTo(dbWorkspace);
dbWorkspace.ModifiedBy = _httpContextAccessor.HttpContext.GetUserId();
dbWorkspace.ModifiedAtUtc = DateTime.UtcNow;
await _provider.SaveAsync();
return(true);
}
public override bool Save(ISession session, DbWorkspace dbWorkspace)
{
var existingModifications = session.CreateCriteria <DbModification>()
.Add(Restrictions.Eq("Workspace", dbWorkspace))
.List <DbModification>()
.ToDictionary(dbModification => dbModification.Symbol);
return(SaveChangedEntities(session, existingModifications,
dbModification => dbModification.DeltaMass,
(dbModification, value) => dbModification.DeltaMass = value,
key => new DbModification
{
Symbol = key,
Workspace = dbWorkspace
}));
}
public override bool Save(ISession session, DbWorkspace dbWorkspace)
{
var existingSettings = session.CreateCriteria <DbSetting>()
.Add(Restrictions.Eq("Workspace", dbWorkspace))
.List <DbSetting>()
.ToDictionary(dbSetting => dbSetting.Name);
return(SaveChangedEntities(session, existingSettings,
dbSetting => dbSetting.Value,
(dbSetting, value) => dbSetting.Value = value,
key => new DbSetting
{
Name = key,
Workspace = dbWorkspace,
}));
}
public override bool Save(ISession session, DbWorkspace dbWorkspace)
{
var existing =
session.CreateCriteria <DbTracerDef>()
.Add(Restrictions.Eq("Workspace", dbWorkspace))
.List <DbTracerDef>()
.ToDictionary(dbTracerDef => dbTracerDef.Name);
return(SaveChangedEntities(session, existing,
dbTracerDef => new TracerDefData(dbTracerDef),
UpdateDbTracerDef,
key => new DbTracerDef
{
Name = key,
Workspace = dbWorkspace,
}));
}
public void OneTimeSetUp()
{
_dbWorkspaceToAdd = new DbWorkspace
{
Name = "Name",
Description = "Description",
IsActive = true,
};
_dbWorkspaceInDb = new DbWorkspace
{
Id = Guid.NewGuid(),
Name = "Name",
IsActive = true
};
CreateMemoryDb();
}
public ShortWorkspaceInfo Map(DbWorkspace dbWorkspace)
{
if (dbWorkspace is null)
{
return(null);
}
return(new ShortWorkspaceInfo
{
Id = dbWorkspace.Id,
Name = dbWorkspace.Name,
Description = dbWorkspace.Description,
IsActive = dbWorkspace.IsActive,
Image = new ImageConsist()
{
Content = dbWorkspace.ImageContent,
Extension = dbWorkspace.ImageExtension
}
});
}
public static void InitWorkspace(ISessionFactory sessionFactory)
{
using (var session = sessionFactory.OpenSession())
{
var transaction = session.BeginTransaction();
var dbWorkspace = new DbWorkspace
{
ModificationCount = 1,
TracerDefCount = 0,
SchemaVersion = WorkspaceUpgrader.CurrentVersion,
};
session.Save(dbWorkspace);
var modification = new DbModification
{
DeltaMass = 57.021461,
Symbol = "C",
Workspace = dbWorkspace
};
session.Save(modification);
transaction.Commit();
}
}
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);
}
// 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 abstract bool Save(ISession session, DbWorkspace dbWorkspace);
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);
}
}
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 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 static void InitWorkspace(ISessionFactory sessionFactory)
{
using (var session = sessionFactory.OpenSession())
{
var transaction = session.BeginTransaction();
var dbWorkspace = new DbWorkspace
{
ModificationCount = 1,
TracerDefCount = 0,
SchemaVersion = WorkspaceUpgrader.CurrentVersion,
};
session.Save(dbWorkspace);
var modification = new DbModification
{
DeltaMass = 57.021461,
Symbol = "C",
Workspace = dbWorkspace
};
session.Save(modification);
transaction.Commit();
}
}
// 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);
}
