public async Task CommitAsync()
{
try
{
// commit transaction if there is one active
if (_transaction != null && _transaction.IsActive)
{
_session.Flush();
_session.Clear();
}
if (_transaction != null)
{
await _transaction.CommitAsync();
}
}
catch
{
// rollback if there was an exception
if (_transaction != null && _transaction.IsActive)
{
await _transaction.RollbackAsync();
}
throw;
}
finally
{
CloseSession();
}
}
public async Task <ActionResult> Post([FromQuery] int zapisid, string filename, DateTime lastmodified, long size, [FromForm] IFormFile file)
{
try
{
var dok = _session.Get <Zapis>(zapisid);
//var kor = _session.QueryOver<Korisnik>()
// .Where(x => x.KorisnickoIme == User.Identity.Name)
// .SingleOrDefault<Korisnik>();
//dok.Rbr = Helper.RedniBroj(_session, "zapis");
using (var ms = new MemoryStream())
{
await file.CopyToAsync(ms);
dok.Data = ms.ToArray();
dok.Size = size;
dok.FileName = filename;
dok.DateLastModified = lastmodified;
}
_session.SaveOrUpdate(dok);
_session.Flush();
return(Json(new { Success = true, Message = "", Objekat = dok }));
}
catch (Exception ex)
{
_logger.LogError(ex.Message);
return(Json(new { Success = false, Message = ex.Message }));
}
}
public CategoryUpdateResponse Update(CategoryUpdateRequest request)
{
var response = new CategoryUpdateResponse();
var existing = CheckForExisting(request.Name);
if (existing != null && existing.Id != request.Id)
{
response.ErrorMessage = "Update would create a duplicate";
}
else
{
var existingById = _categoryRepository.Get(request.Id);
if (existingById == null)
{
response.ErrorMessage = "Category not found";
}
else
{
_session.Flush();
existingById.Name = request.Name;
existingById.LastUpdate = DateTime.UtcNow;
_categoryRepository.Update(existingById);
response.Category = new Category()
{
Id = existingById.Id,
Name = existingById.Name,
LastUpdate = existingById.LastUpdate
};
}
}
return(response);
}
public void AfterInvoke(object correlationState)
{
foreach (ISessionFactory sessionFactory in sfp)
{
ISession session = CurrentSessionContext.Unbind(sessionFactory);
if (!session.IsOpen)
{
continue;
}
try
{
session.Flush();
if (session.Transaction.IsActive)
{
session.Transaction.Commit();
}
}
catch (Exception)
{
if (session.Transaction.IsActive)
{
session.Transaction.Rollback();
}
throw;
}
finally
{
session.Close();
session.Dispose();
}
}
}
public FilmCreateResponse Add(FilmCreateRequest request)
{
var response = new FilmCreateResponse();
// Get language
var lang = _languageRepository.Get(request.Film.LanguageId);
var origLang = _languageRepository.Get(request.Film.OriginalLanguageId ?? 0);
var film = new en.Film
{
Language = lang,
OriginalLanguage = origLang,
Title = request.Film.Title,
Description = request.Film.Description,
ReleaseYear = request.Film.ReleaseYear,
RentalDuration = request.Film.RentalDuration,
Length = request.Film.Length,
RentalRate = request.Film.RentalRate,
Rating = request.Film.Rating,
SpecialFeatures = request.Film.SpecialFeatures,
ReplacementCost = request.Film.ReplacementCost,
LastUpdate = DateTime.Now
};
_session.Save(film);
_session.Flush();
response.Film = request.Film;
response.Film.Id = film.Id;
response.Film.LastUpdate = film.LastUpdate;
return(response);
}
public async Task <ActionResult> Post([FromQuery] string entitet, int entitetid, string entitetopis, string filename, DateTime lastmodified, long size, [FromForm] IFormFile file)
{
try
{
var dok = new Dokument()
{
FileName = filename, Entitet = entitet, EntitetId = entitetid, EntitetOpis = entitetopis, DateLastModified = lastmodified, Size = size
};
using (var ms = new MemoryStream())
{
await file.CopyToAsync(ms);
dok.Data = ms.ToArray();
dok.DateLastModified = lastmodified;
}
_session.SaveOrUpdate(dok);
_session.Flush();
return(Json(new { Success = true, Message = "" }));
}
catch (Exception ex)
{
_logger.LogError(ex.Message);
return(Json(new { Success = false, Message = ex.Message }));
}
}
public object Save <T>(T entity) where T : class
{
NH.ISession session = Session;
object obj = session.Save(entity);
session.Flush();
return(obj);
}
public IActionResult Edit(Edit mdl)
{
User uID = _session.Get <User>(mdl.Id);
using (var txn = _session.BeginTransaction())
{
uID.Id = mdl.Id;
uID.Username = mdl.UserName;
uID.Password = mdl.Password;
uID.Email = mdl.Email;
uID.DOB = mdl.DOB;
uID.Country = mdl.Country;
uID.Bio = mdl.Bio;
_session.SaveOrUpdate(uID);
_session.Flush();
txn.Commit();
}
return(RedirectToAction("Index"));
}
private void MvcApplication_EndRequest(object sender, System.EventArgs e)
{
if (Context.Items.Contains(NHibernateModule.SESSION_KEY))
{
Debug.WriteLine("Disposing the NHibernate session");
NHibernate.ISession Session = (NHibernate.ISession)Context.Items[NHibernateModule.SESSION_KEY];
Session.Flush();
Session.Dispose();
Context.Items[NHibernateModule.SESSION_KEY] = null;
}
}
public static void flushAndDisposeSession()
{
NHibernate.ISession currentSession = getCurrentSession();
currentSession.Flush();
//currentSession.Close();
currentSession.Dispose();
var context = httpContextAccessor.HttpContext;
context.Items.Remove(CurrentSessionKey);
}
public IActionResult Edit(Edit mdl)
{
Movie mID = _session.Get <Movie>(mdl.Id);
Review review = mID.Reviews.SingleOrDefault(r => r.User.Id == _context.UserId);
using (var txn = _session.BeginTransaction())
{
mID.Id = mdl.Id;
mID.MovieName = mdl.MovieName;
mID.LengthInMin = mdl.LengthInMin;
mID.Summary = mdl.Summary;
mID.Year = mdl.Year;
mID.Genre = mdl.Genre;
mID.ContentRating = mdl.ContentRating;
mID.Language = mdl.Language;
review.Rating = mdl.Rating;
review.ReviewText = mdl.ReviewText;
//_session.SaveOrUpdate(mID);
_session.Flush();
txn.Commit();
}
return(RedirectToAction("Index"));
}
public ActionResult BrisiUplatu(int id)
{
//this.repo.find("Dokument?entitet=" + entitet + "&entitetopis=" + entitetoipis + "&entitetid" + entitet)
try
{
var obj = _session.Load <Uplata>(id);
obj.Obrisan = true;
_session.SaveOrUpdate(obj);
_session.Flush();
return(Json(new { Success = true, Message = "", obj = true }));
}
catch (Exception ex)
{
_logger.LogError(ex.Message);
return(Json(new { Success = false, Message = ex.Message }));
}
}
public void SaveOrUpdate <T>(T entity) where T : class
{
NH.ISession session = Session;
session.SaveOrUpdate(entity);
session.Flush();
}
public void Delete <T>(T entity) where T : class
{
NH.ISession session = Session;
session.Delete(entity);
session.Flush();
}
void OpenFiles (IList<string> filepaths, TreeNode rootNode = null)
{
try
{
var xml_filepaths = filepaths.Where(filepath => !filepath.EndsWith(".idpDB"));
var idpDB_filepaths = filepaths.Where(filepath => filepath.EndsWith(".idpDB"));
bool openSingleFile = xml_filepaths.Count() + idpDB_filepaths.Count() == 1;
if (xml_filepaths.Count() + idpDB_filepaths.Count() == 0)
{
if (Program.IsHeadless)
{
Console.Error.WriteLine("Headless mode must be passed some idpDB files to merge.");
Close();
return;
}
else
throw new Exception("no filepaths to open");
}
if (Program.IsHeadless && xml_filepaths.Any())
Program.HandleUserError(new Exception("headless mode only supports merging and filtering idpDB files"));
// warn if idpDBs already exist
bool warnOnce = false, skipReconvert = false;
var skipFiles = new List<string>();
foreach (string filepath in xml_filepaths)
{
string idpDB_filepath = Path.ChangeExtension(filepath.Replace(".pep.xml", ".pepXML"), ".idpDB");
if (File.Exists(idpDB_filepath))
{
if (!warnOnce && MessageBox.Show("Some of these files have already been converted. Do you want to reconvert them?",
"Result already converted",
MessageBoxButtons.YesNo,
MessageBoxIcon.Exclamation,
MessageBoxDefaultButton.Button2) != DialogResult.Yes)
skipReconvert = true;
warnOnce = true;
if (skipReconvert)
skipFiles.Add(filepath);
else
File.Delete(idpDB_filepath);
}
}
xml_filepaths = xml_filepaths.Where(o => !skipFiles.Contains(o));
idpDB_filepaths = idpDB_filepaths.Union(skipFiles.Select(o => Path.ChangeExtension(o.Replace(".pep.xml", ".pepXML"), ".idpDB")));
// determine if merged filepath exists and that it's a valid idpDB
var potentialPaths = filepaths.Select(item =>
Path.Combine(Path.GetDirectoryName(item) ?? string.Empty,
Path.GetFileNameWithoutExtension(item) ??
string.Empty) + ".idpDB").ToList();
// for Mascot files (*.dat), use parseSource() to get the real filename, else save time by just using filename without extension
var sourceNames = filepaths.Select(o => Path.Combine(Path.GetDirectoryName(o), o.ToLower().EndsWith(".dat") ? Parser.ParseSource(o) : Path.GetFileNameWithoutExtension(o.Replace(".pep.xml", ".pepXML")) + Path.GetExtension(o)));
string commonFilepath = Util.GetCommonFilename(sourceNames);
if (!openSingleFile && potentialPaths.Contains(commonFilepath))
commonFilepath = commonFilepath.Replace(".idpDB", " (merged).idpDB");
string mergeTargetFilepath = defaultMergedOutputFilepath ?? commonFilepath;
if (!openSingleFile && File.Exists(mergeTargetFilepath) && Program.IsHeadless)
File.Delete(mergeTargetFilepath);
else
{
// check that the single idpDB is writable; if not, it needs to be copied
if (openSingleFile)
{
// sanity check that file exists after the path manipulation above
if (idpDB_filepaths.Count() == 1 && !File.Exists(mergeTargetFilepath))
throw new Exception(String.Format("error in internal path manipulation for opening single idpDB: {0} transformed to {1} which does not exist", sourceNames.First(), mergeTargetFilepath));
string oldFilename = mergeTargetFilepath;
while (true)
{
if (canReadWriteInDirectory(Path.GetDirectoryName(mergeTargetFilepath)))
break;
MessageBox.Show("IDPicker files cannot be opened from a read-only location, pick a writable path to copy it to.");
if (!saveFileDialog(ref mergeTargetFilepath))
return;
}
// if location was changed, copy to the new location
if (oldFilename != mergeTargetFilepath)
{
toolStripStatusLabel.Text = "Copying idpDB...";
File.Copy(oldFilename, mergeTargetFilepath, true);
}
}
else
{
// if not headless and MergedOutputFilepath is unset,
// then give the user a chance to override the merge target location
if (!Program.IsHeadless &&
defaultMergedOutputFilepath == null &&
!saveFileDialog(ref mergeTargetFilepath, "Choose where to create the merged idpDB"))
return;
while (true)
{
if (!canReadWriteInDirectory(Path.GetDirectoryName(mergeTargetFilepath)))
{
MessageBox.Show("IDPicker files cannot be merged to a read-only location, pick a writable path.");
if (Program.IsHeadless || !saveFileDialog(ref mergeTargetFilepath, "Pick a writable path in which to create the merged idpDB"))
return;
continue;
}
// the SaveFileDialog already asked the user to confirm overwriting an existing file
if (File.Exists(mergeTargetFilepath))
File.Delete(mergeTargetFilepath);
break;
}
}
}
// set main window title
BeginInvoke(new MethodInvoker(() => Text = mergeTargetFilepath));
//set up delayed messages so non-fatal errors that occur at the end arent lost
var delayedMessages = new List<string[]>();
if (xml_filepaths.Count() > 0)
{
importCancelled = false;
// loop until the import settings don't result in any fatal errors, or user cancels
while (!importCancelled)
{
Parser parser = new Parser();
Invoke(new MethodInvoker(() => parser.ImportSettings += importSettingsHandler));
var ilr = new IterationListenerRegistry();
var progressForm = new ProgressForm(xml_filepaths, ilr)
{
Text = "Import Progress",
StartPosition = FormStartPosition.CenterParent,
};
Invoke(new MethodInvoker(() => progressForm.Show(this)));
try
{
parser.Parse(xml_filepaths, ilr);
// read log for non-fatal errors
//string log = Logger.Reader.ReadToEnd().Trim();
//if (log.Length > 0)
// Invoke(new MethodInvoker(() => UserDialog.Show(this, "Log Messages", new TextBox {Multiline = true, Text = log.Replace("\n", "\r\n"), ReadOnly = true, Size = new Size(800, 600), ScrollBars = ScrollBars.Both}, MessageBoxButtons.OK)));
break; // no fatal errors, break the loop
}
catch (Exception ex)
{
if (ex.Message.Contains("no peptides found mapping to a decoy protein") ||
ex.Message.Contains("peptides did not map to the database") ||
ex.Message.Contains("duplicate protein id"))
Program.HandleUserError(ex);
else
throw;
}
finally
{
importCancelled |= progressForm.Cancelled;
Invoke(new MethodInvoker(() => progressForm.Close()));
}
}
if (importCancelled)
return;
idpDB_filepaths = idpDB_filepaths.Union(xml_filepaths.Select(o => Path.ChangeExtension(o.Replace(".pep.xml", ".pepXML"), ".idpDB")));
}
if (idpDB_filepaths.Count() > 1)
{
var merger = new MergerWrapper(mergeTargetFilepath, idpDB_filepaths);
toolStripStatusLabel.Text = "Merging results...";
merger.MergingProgress += progressMonitor.UpdateProgress;
merger.Start();
idpDB_filepaths = new List<string>() {mergeTargetFilepath};
}
// HACK: this needs to be handled more gracefully
if (!IsHandleCreated)
return;
if (Properties.GUI.Settings.Default.WarnAboutNonFixedDrive && !Util.IsPathOnFixedDrive(mergeTargetFilepath))
{
string oldFilename = mergeTargetFilepath;
bool copyLocal = true;
Invoke(new MethodInvoker(() =>
{
var form = new NonFixedDriveWarningForm();
if (form.ShowDialog(this) == DialogResult.Ignore)
copyLocal = false;
}));
if (copyLocal)
{
string newFilename = Path.GetFileName(mergeTargetFilepath);
if (!saveFileDialog(ref newFilename, "Pick a local path to copy the idpDB to"))
return;
toolStripStatusLabel.Text = "Copying idpDB...";
File.Copy(oldFilename, newFilename, true);
mergeTargetFilepath = newFilename;
// set main window title
BeginInvoke(new MethodInvoker(() => Text = mergeTargetFilepath));
}
}
if (!IsHandleCreated)
return;
Util.PrecacheFile(mergeTargetFilepath, progressMonitor.UpdateProgress);
if (!IsHandleCreated)
return;
BeginInvoke(new MethodInvoker(() =>
{
clearProgress();
toolStripStatusLabel.Text = "Upgrading schema and creating session factory...";
statusStrip.Refresh();
}));
var sessionFactory = DataModel.SessionFactoryFactory.CreateSessionFactory(mergeTargetFilepath, new SessionFactoryConfig { WriteSqlToConsoleOut = true });
if (logForm != null) logForm.SetSessionFactory(sessionFactory);
BeginInvoke(new MethodInvoker(() =>
{
// reload qonverter settings because the ids may change after merging
toolStripStatusLabel.Text = "Loading qonverter settings...";
statusStrip.Refresh();
session = sessionFactory.OpenSession();
session.DefaultReadOnly = true;
session.CreateSQLQuery("PRAGMA temp_store=MEMORY; PRAGMA mmap_size=70368744177664; -- 2^46").ExecuteUpdate();
toolStripStatusLabel.Text = "Refreshing group structure...";
statusStrip.Refresh();
var usedGroups = GroupingControlForm.SetInitialStructure(rootNode, session, defaultApplySourceGroupHierarchy);
if (usedGroups != null && usedGroups.Any())
{
var allGroupsByName = session.Query<SpectrumSourceGroup>().ToDictionary(o => o.Name);
var usedGroupsByName = usedGroups.ToDictionary(o => o.Name);
// if usedGroupsByName does not contain a key from allGroupsByName, delete the group
foreach (var unusedGroup in allGroupsByName.Where(o => !usedGroupsByName.ContainsKey(o.Key)))
session.Delete(unusedGroup);
}
session.Flush();
// check for embedded gene metadata;
// if it isn't there, ask the user if they want to embed it;
// if not, disable gene-related features
if (!Program.IsHeadless && !Embedder.HasGeneMetadata(mergeTargetFilepath) && Properties.GUI.Settings.Default.WarnAboutNoGeneMetadata)
{
bool embedGeneMetadata = true;
Invoke(new MethodInvoker(() =>
{
var form = new EmbedGeneMetadataWarningForm();
if (form.ShowDialog(this) == DialogResult.Ignore)
embedGeneMetadata = false;
}));
if (embedGeneMetadata)
{
loadRefSeqGeneMetadata(); // will call OpenFiles() after embedding, so return immediately
return;
}
}
else
{
// disable gene-related features
}
qonverterSettingsByAnalysis = session.Query<QonverterSettings>().ToDictionary(o => session.Get<Analysis>(o.Id));
_layoutManager.SetSession(session);
//set or save default layout
dockPanel.Visible = true;
_layoutManager.CurrentLayout = _layoutManager.GetCurrentDefault();
//breadCrumbControl.BreadCrumbs.Clear();
// pick a default RoundToNearest based on number of distinct modifications
decimal roundToNearest = 1m;
var distinctModificationFormat = new DistinctMatchFormat();
var modMasses = session.CreateQuery("SELECT DISTINCT mod.MonoMassDelta FROM Modification mod").List<double>();
for (int i = 4; i > 0; --i)
{
distinctModificationFormat.ModificationMassRoundToNearest = (decimal) (1.0 / Math.Pow(10, i));
if (modMasses.Select(o => distinctModificationFormat.Round(o)).Distinct().Count() < 30)
{
roundToNearest = distinctModificationFormat.ModificationMassRoundToNearest.Value;
break;
}
}
modificationTableForm.RoundToNearest = roundToNearest;
basicFilter = DataFilter.LoadFilter(session);
// if user has overridden filters from the command-line, make sure to reapply the filter
if (!defaultDataFilter.PersistentDataFilter.Equals(defaultDataFilter.OriginalPersistentDataFilter))
basicFilter = null;
if (basicFilter == null)
{
basicFilter = new DataFilter(defaultDataFilter);
basicFilterControl.DataFilter = basicFilter;
viewFilter = basicFilter;
ApplyBasicFilter();
}
else
{
basicFilterControl.DataFilter = basicFilter;
viewFilter = basicFilter;
try
{
// check that the unfiltered tables exist
session.CreateSQLQuery("SELECT COUNT(*) FROM UnfilteredProtein").UniqueResult();
setData();
}
catch
{
ApplyBasicFilter();
}
}
if (TestUILayout)
{
int i = 0;
foreach(var form in dockPanel.Contents)
{
++i;
form.DockingHandler.DockAreas = (form.DockingHandler.DockAreas | DockAreas.Float);
var rect = dockPanel.ClientRectangle;
rect.Offset(i * 15, i * 15);
rect.Size = new System.Drawing.Size(960, 600);
form.DockingHandler.Show(dockPanel, rect);
}
}
toolStripStatusLabel.Text = "Ready";
Activate();
}));
//show list of delayed non-fatal errors
if (delayedMessages.Any())
{
var sb = new StringBuilder();
foreach (var message in delayedMessages)
sb.AppendLine(string.Format("{0}:{1}{2}{1}", message[0], Environment.NewLine, message[1]));
var messageString = sb.ToString();
ShowExpandedMessageBox(messageString);
}
}
catch (Exception ex)
{
Program.HandleException(ex);
}
}
public void Commit()
{
session.Flush();
}
private static void OptionsScreen(NHibernate.ISession session)
{
Console.WriteLine("Recepie Database.");
Console.WriteLine();
Console.WriteLine("Make a choise: ");
Console.WriteLine("[1] Create new recepie");
Console.WriteLine("[2] Remove recepie");
Console.WriteLine("[3] Update recepie");
Console.WriteLine("[4] Display all recepies");
Console.WriteLine("[5] Search recepies by category");
Console.WriteLine("[6] Search recepies by ingredient");
//Console.WriteLine("[S]earch recepies by recepie name");
Console.WriteLine("[7] Generate new recepielist");
Console.WriteLine("[8] Display all recepielists");
Console.WriteLine("[F]ill with testdata");
Console.WriteLine("[D]elete entire database ");
Console.WriteLine("[C]reate database");
Console.WriteLine("[Q]uit");
Console.Write("");
string choise = Console.ReadLine();
switch (choise.ToUpper())
{
case "1":
CreateNewRecepie(session);
OptionsScreen(session);
break;
case "2":
RemoveRecepie();
OptionsScreen(session);
break;
case "3":
UpdateRecepie();
OptionsScreen(session);
break;
case "4":
session.Flush();
DisplayRecepies(session);
break;
case "5":
DisplayRecepiesByCategory(session);
break;
case "6":
DisplayRecepiesByIngredient(session);
break;
//case "S":
// SearchRecepies();
// DisplayRecepieProperties(session);
// break;
case "7":
GenerateRecepielist(session);
OptionsScreen(session);
break;
case "8":
DispalyRecepieLists(session);
OptionsScreen(session);
break;
case "F":
GenerateTestData(session);
OptionsScreen(session);
break;
case "D":
DeleteDatabase();
session.Flush();
OptionsScreen(session);
break;
case "C":
CreateDatabase();
session.Flush();
OptionsScreen(session);
break;
case "Q":
DbService.CloseSession(session);
break;
default:
OptionsScreen(session);
break;
}
}