public ActionResult Datumi() //[Microsoft.AspNetCore.Mvc.FromBody] DatumiUlazniPodaci par
{
var query = _session.CreateSQLQuery("exec datumi");
//query.SetParameter("period", par?.Period, NHibernateUtil.Int32);
//query.SetParameter("zavrsen", par?.Zavrsen, NHibernateUtil.Boolean);
query.SetResultTransformer(new AliasToBeanResultTransformer(typeof(DatumiIzlazniPodaci)));
var res = query.List <DatumiIzlazniPodaci>();
return(Ok(res));
}
/// <getTasksByUserwithDetail>
/// Get Tasks By User with Detail
/// </summary>
/// <param name="USerId">User id.(Guid)</param>
/// <param name="days">Number of Days.(int)</param>
/// <returns>Return values in the form of array list.(ArrayList)</returns>
public ArrayList getTasksByUserwithDetail(Guid USerId, int days, Guid GroupId)
{
//Creates a database connection and opens up a session
using (NHibernate.ISession session = SessionFactory.GetNewSession())
{
//After Session creation, start Transaction.
using (NHibernate.ITransaction transaction = session.BeginTransaction())
{
//Proceed action, to get details of task. //ts.UserId=:userid and //.SetParameter("userid", USerId)
//var queryString = @"SELECT * FROM Tasks ts LEFT JOIN User u on ts.AssignTaskTo=u.Id where ts.UserId=:userid and AssignDate>=DATE_ADD(NOW(),INTERVAL -" + days + " DAY)";
//var queryString = @"SELECT * FROM Tasks ts LEFT JOIN User u on ts.AssignTaskTo=u.Id where ts.GroupId=:GroupId and AssignDate>=DATE_ADD(NOW(),INTERVAL -" + days + " DAY)";
try
{
var queryString = @"select * from tasks where (AssignTaskTo =:userid or UserId =:userid) and GroupId =:GroupId and AssignDate>=DATE_ADD(NOW(),INTERVAL -" + days + " DAY)";
var query = session.CreateSQLQuery(queryString)
.SetParameter("userid", USerId)
.SetParameter("GroupId", GroupId);
//.SetParameter("GroupId", GroupId);
ArrayList alstTask = new ArrayList();
foreach (var item in query.List())
{
alstTask.Add(item);
}
return(alstTask);
}
catch (Exception)
{
throw;
}
} //End Transaction
} //End Session
}
public ActionResult Rekapitulacija(DateTime?dat1, DateTime?dat2, int klijentid, int ponudaid, int radninalogid)
{
try
{
var upit = _session.CreateSQLQuery("exec rekapitulacija :dat1, :dat2, :klijentid, :ponudaid, :radninalogid")
.SetParameter("dat1", null, NHibernateUtil.Date)
.SetParameter("dat2", null, NHibernateUtil.Date)
.SetParameter("klijentid", null, NHibernateUtil.Int32)
.SetParameter("ponudaid", null, NHibernateUtil.Int32)
.SetParameter("radninalogid", null, NHibernateUtil.Int32);
if (dat1.HasValue)
{
upit.SetParameter("dat1", dat1.Value, NHibernateUtil.Date);
}
if (dat2.HasValue)
{
upit.SetParameter("dat2", dat2.Value, NHibernateUtil.Date);
}
if (klijentid != 0)
{
upit.SetParameter("klijentid", klijentid, NHibernateUtil.Int32);
}
if (ponudaid != 0)
{
upit.SetParameter("ponudaid", ponudaid, NHibernateUtil.Int32);
}
if (radninalogid != 0)
{
upit.SetParameter("radninalogid", radninalogid, NHibernateUtil.Int32);
}
var rekap = upit.SetResultTransformer(new AliasToBeanResultTransformer(typeof(Rekapitulacija)))
.UniqueResult <Rekapitulacija>();
return(Json(new { Success = true, Message = "", obj = rekap }));
}
catch (Exception ex)
{
_logger.LogError(ex.Message);
return(Json(new { Success = false, Message = ex.Message }));
}
}
public void Drop()
{
SqlConnection.ClearAllPools();
using (ISessionFactory sessionFactory = masterConfiguration.BuildSessionFactory())
{
using (INHSession session = sessionFactory.OpenSession())
{
var query = session.CreateSQLQuery("DROP DATABASE ContactBook;");
var result = query.ExecuteUpdate();
}
}
}
public Korisnik KorisnikPostoji(string korisnickoIme)
{
var query = _session.CreateSQLQuery("exec KorisnikPostoji :korisnickoime");
query.SetParameter("korisnickoime", korisnickoIme, NHibernateUtil.String);
query.AddEntity(typeof(Korisnik));
return(query.UniqueResult <Korisnik>());
}
public void Create()
{
using (ISessionFactory sessionFactory = masterConfiguration.BuildSessionFactory())
{
using (INHSession session = sessionFactory.OpenSession())
{
var query = session.CreateSQLQuery("CREATE DATABASE ContactBook;");
var result = query.ExecuteUpdate();
}
}
var schemaExport = new SchemaExport(configuration);
schemaExport.Create(false, true);
}
public ActionResult Brisi(int id)
{
//this.repo.find("Dokument?entitet=" + entitet + "&entitetopis=" + entitetoipis + "&entitetid" + entitet)
try
{
var sql = _session.CreateSQLQuery("exec BrisiDokument :id");
sql.SetParameter("id", id, NHibernateUtil.Int32);
var ret = sql.ExecuteUpdate();
return(Json(new { Success = true, Message = "", obj = ret }));
}
catch (Exception ex)
{
_logger.LogError(ex.Message);
return(Json(new { Success = false, Message = ex.Message }));
}
}
public void DeleteSelectRows(GroupCampaign ObjGrpCamp)
{
try
{
using (NHibernate.ISession session = SessionFactory.GetNewSession())
{
using (NHibernate.ITransaction transaction = session.BeginTransaction())
{
var query = session.CreateSQLQuery("delete from GroupCampaign WHERE GroupCampaignName = :CampaignName and Module =:module").SetParameter("CampaignName", ObjGrpCamp.GroupCampaignName).SetParameter("module", ObjGrpCamp.Module);
int res = query.ExecuteUpdate();
transaction.Commit();
}
}
}
catch (Exception ex)
{
GlobusLogHelper.log.Error("Error : " + ex.StackTrace);
}
}
public ArrayList UnPaidUserCountByMonth()
{
using (NHibernate.ISession session = SessionFactory.GetNewSession())
{
using (NHibernate.ITransaction transaction = session.BeginTransaction())
{
ArrayList alstUser = new ArrayList();
try
{
NHibernate.IQuery query = session.CreateSQLQuery("Select month(CreateDate),Count(*) from User where PaymentStatus='unpaid' group by month(CreateDate)");
foreach (var item in query.List())
{
alstUser.Add(item);
}
return(alstUser);
}
catch (Exception Err)
{
Console.Write(Err.StackTrace);
return(alstUser);
}
}
}
}
public ISQLQuery CreateSQLQuery(string q)
{
return(_session.CreateSQLQuery(q));
}
void setData(object sender, DoWorkEventArgs e)
{
try
{
Map <int, List <PSMRow> > precursorMassErrorsByCharge = new Map <int, List <PSMRow> >();;
IDictionary <int, int> spectralCountByChargeState;
lock (session)
{
var randomIds = session.CreateQuery("SELECT psm.Id " + viewFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch))
.List <long>()
.Shuffle()
.Take(50000)
.OrderBy(o => o);
string randomIdSet = String.Join(",", randomIds.Select(o => o.ToString()).ToArray());
var query = session.CreateSQLQuery("SELECT psm.ObservedNeutralMass, psm.MonoisotopicMassError, psm.MolecularWeightError, s.ScanTimeInSeconds, psm.Charge " +
"FROM PeptideSpectrumMatch psm " +
"JOIN Spectrum s ON psm.Spectrum=s.Id " +
"WHERE psm.Id IN (" + randomIdSet + ") " +
"GROUP BY psm.Id");
query.List <object[]>().ForEach(o =>
precursorMassErrorsByCharge[Convert.ToInt32(o[4])].Add(new PSMRow
{
ObservedNeutralMass = Convert.ToDouble(o[0]),
MassError = PeptideSpectrumMatch.GetSmallerMassError(Convert.ToDouble(o[1]), Convert.ToDouble(o[2])),
ScanTime = Convert.ToDouble(o[3]) / 60, // convert to minutes
Charge = Convert.ToInt32(o[4])
}));
var query2 = session.CreateQuery("SELECT psm.Charge, COUNT(DISTINCT psm.Spectrum.id) " +
dataFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch) +
"GROUP BY psm.Charge");
spectralCountByChargeState = query2.List <object[]>().ToDictionary(o => Convert.ToInt32(o[0]), o => Convert.ToInt32(o[1]));
}
Map <int, List <List <PSMRow> > > clusteredPrecursorMassErrorsByCharge = clusterMassErrors(precursorMassErrorsByCharge);
// convert to PPM if the user requested it
if (!ppmMassErrorMenuItem.Text.Contains("PPM"))
{
clusteredPrecursorMassErrorsByCharge.Values.ForEach(o3 => o3.ForEach(o2 => o2.ForEach(o => o.MassError = o.MassError / o.ObservedNeutralMass * 1e6)));
}
{
var csr = new ColorSymbolRotator();
precursorMassErrorForm.ZedGraphControl.GraphPane.CurveList.Clear();
foreach (var kvp in clusteredPrecursorMassErrorsByCharge)
{
bool firstCluster = true;
var color = csr.NextColor;
foreach (var precursorMassErrorCluster in kvp.Value)
{
var precursorMassErrors = precursorMassErrorCluster;
var precursorMassErrorValues = precursorMassErrors.Select(o => o.MassError).ToArray();
var densityCurve = new LineItem(firstCluster ? kvp.Key.ToString() : "", getDensityCurve(precursorMassErrorValues, 0), color, SymbolType.None);
var grassPlot = new LineItem("", precursorMassErrorValues, Enumerable.Repeat(0.0, precursorMassErrorValues.Length).ToArray(), color, SymbolType.VDash)
{
Tag = kvp.Key
};
densityCurve.Line.IsAntiAlias = true;
precursorMassErrorForm.ZedGraphControl.GraphPane.CurveList.Add(densityCurve);
precursorMassErrorForm.ZedGraphControl.GraphPane.CurveList.Add(grassPlot);
firstCluster = false;
}
}
}
{
var csr = new ColorSymbolRotator();
scanTimeDistributionForm.ZedGraphControl.GraphPane.CurveList.Clear();
foreach (var kvp in precursorMassErrorsByCharge)
{
var precursorMassErrors = kvp.Value;
var scanTimeValues = precursorMassErrors.Select(o => o.ScanTime).ToList();
var color = csr.NextColor;
if (scanTimeValues.Max() > 0)
{
var densityCurve = new LineItem(kvp.Key.ToString(), getDensityCurve(scanTimeValues, 0), color, SymbolType.None);
var grassPlot = new LineItem("", scanTimeValues.ToArray(), Enumerable.Repeat(0.0, scanTimeValues.Count).ToArray(), color, SymbolType.VDash);
densityCurve.Line.IsAntiAlias = true;
scanTimeDistributionForm.ZedGraphControl.GraphPane.CurveList.Add(densityCurve);
scanTimeDistributionForm.ZedGraphControl.GraphPane.CurveList.Add(grassPlot);
}
}
if (scanTimeDistributionForm.ZedGraphControl.GraphPane.CurveList.IsNullOrEmpty())
{
scanTimeDistributionForm.ZedGraphControl.GraphPane.GraphObjList.Add(
new TextObj("No scan time information present.\r\nUse File/Embed to import scan times from raw data.",
0.5, 0.5, CoordType.ChartFraction, AlignH.Center, AlignV.Center)
{
FontSpec = new FontSpec("monospace", 18.0f, Color.Black, true, false, false)
});
}
}
var colorRotator = new ColorSymbolRotator();
var colors = new List <Color>();
foreach (var kvp in spectralCountByChargeState)
{
colors.Add(colorRotator.NextColor);
}
chargeStatesForm.ZedGraphControl.GraphPane.CurveList.Clear();
chargeStatesForm.ZedGraphControl.GraphPane.BarSettings.MinClusterGap = 8;
var barItem = chargeStatesForm.ZedGraphControl.GraphPane.AddBar("", spectralCountByChargeState.Keys.Select(o => (double)o).ToArray(), spectralCountByChargeState.Values.Select(o => (double)o).ToArray(), Color.White) as BarItem;
for (int i = 0; i < barItem.Points.Count; ++i)
{
barItem.Points[i].ColorValue = (double)i + 1;
}
barItem.Bar.Fill = new Fill(colors.ToArray())
{
Type = FillType.GradientByColorValue,
RangeMin = 1,
RangeMax = colors.Count
};
chargeStatesForm.ZedGraphControl.GraphPane.XAxis.Scale.TextLabels = spectralCountByChargeState.Keys.Select(o => o.ToString()).ToArray();
}
catch (Exception ex)
{
e.Result = ex;
}
}
private static void TestIdentityOff(NHibernate.ISession session, string tableName)
{
var sqlQry = session.CreateSQLQuery(@"SET IDENTITY_INSERT TestService.dbo." + tableName + " OFF");
sqlQry.UniqueResult();
}
public void ApplyQonverterSettings(IDictionary<Analysis, QonverterSettings> qonverterSettings)
{
clearData();
setControlsWhenDatabaseLocked(true);
var workerThread = new BackgroundWorker()
{
WorkerReportsProgress = true,
WorkerSupportsCancellation = true
};
workerThread.DoWork += (s, e) =>
{
var qonverter = new Qonverter();
qonverter.QonversionProgress += progressMonitor.UpdateProgress;
foreach (var item in qonverterSettings)
qonverter.SettingsByAnalysis[(int) item.Key.Id] = item.Value.ToQonverterSettings();
//qonverter.LogQonversionDetails = true;
qonverter.Reset(Text);
qonverter.Qonvert(Text);
};
workerThread.RunWorkerCompleted += (s, e) =>
{
if (e.Result is Exception)
{
Program.HandleException(e.Result as Exception);
setControlsWhenDatabaseLocked(false);
return;
}
lock (session)
{
var sessionFactory = DataModel.SessionFactoryFactory.CreateSessionFactory(Text, new SessionFactoryConfig { WriteSqlToConsoleOut = true });
session = sessionFactory.OpenSession();
//session.CreateSQLQuery("PRAGMA temp_store=MEMORY").ExecuteUpdate();
_layoutManager.SetSession(session);
// delete old filters since they are not valid with different qonverter settings
session.CreateSQLQuery("DELETE FROM FilterHistory").ExecuteUpdate();
session.Clear();
if (basicFilter == null)
basicFilter = new DataFilter()
{
MaximumQValue = 0.02,
MinimumDistinctPeptides = 2,
MinimumSpectra = 2,
MinimumAdditionalPeptides = 1,
GeneLevelFiltering = false,
DistinctMatchFormat = new DistinctMatchFormat
{
IsChargeDistinct = true,
IsAnalysisDistinct = false,
AreModificationsDistinct = true,
ModificationMassRoundToNearest = 1.0m
}
};
basicFilterControl.DataFilter = basicFilter;
viewFilter = basicFilter;
session.Close();
sessionFactory.Close();
}
progressMonitor = new ProgressMonitor();
progressMonitor.ProgressUpdate += progressMonitor_ProgressUpdate;
basicFilterControl = new BasicFilterControl();
basicFilterControl.BasicFilterChanged += basicFilterControl_BasicFilterChanged;
basicFilterControl.ShowQonverterSettings += ShowQonverterSettings;
dataFilterPopup = new Popup(basicFilterControl) { FocusOnOpen = true };
dataFilterPopup.Closed += dataFilterPopup_Closed;
new Thread(() => OpenFiles(new List<string> { Text }, null)).Start();
};
workerThread.RunWorkerAsync();
}
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);
}
}