public ProgressForm(IEnumerable <string> taskNames, IterationListenerRegistry ilr)
{
InitializeComponent();
_progressCellByTaskName = new Dictionary <string, DataGridViewProgressCell>();
_textBoxLogByTaskName = new Dictionary <string, TextBox>();
_lastMessageByTaskName = new Dictionary <string, string>();
_rowByTaskName = new Dictionary <string, DataGridViewRow>();
_tasksDone = 0;
_ilr = ilr;
_ilProxy = new IterationListenerProxy()
{
form = this
};
_ilr.addListener(_ilProxy, 1000);
var boxShown = false;
foreach (var task in taskNames)
{
var textBox = _textBoxLogByTaskName[task] = new TextBox
{
Text = String.Format("{0}{1}{0}Starting...{0}",
Environment.NewLine,
new string('-', 30)),
Dock = DockStyle.Fill,
Multiline = true,
ScrollBars = ScrollBars.Vertical
};
if (boxShown)
{
textBox.Visible = false;
}
else
{
textBox.Visible = true;
boxShown = true;
}
ProgressSplit.Panel2.Controls.Add(textBox);
JobDataView.Rows.Add(task, 0);
var row = JobDataView.Rows[JobDataView.Rows.Count - 1];
row.Tag = textBox;
_rowByTaskName[task] = row;
_progressCellByTaskName[task] = row.Cells[1] as DataGridViewProgressCell;
_progressCellByTaskName[task].Text = "waiting";
}
}
void processFile(string filename, Config config, ReaderList readers)
{
// read in data file
using (var msdList = new MSDataList())
{
string msg = String.Format("Opening file \"{0}\" for read...", filename);
if (LogUpdate != null)
{
LogUpdate(msg, _info);
}
if (StatusUpdate != null)
{
StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
}
readers.read(filename, msdList);
foreach (var msd in msdList)
{
var outputFilename = config.outputFilename(filename, msd);
if (filename == outputFilename)
{
throw new ArgumentException("Output filepath is the same as input filepath");
}
if (StatusUpdate != null)
{
StatusUpdate("Waiting...", ProgressBarStyle.Marquee, _info);
}
// only one thread
lock (calculateSHA1Mutex)
{
if (LogUpdate != null)
{
LogUpdate("Calculating SHA1 checksum...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
}
MSDataFile.calculateSHA1Checksums(msd);
}
if (LogUpdate != null)
{
LogUpdate("Processing...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info);
}
SpectrumListFactory.wrap(msd, config.Filters);
if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty())
{
if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty())
{
msg = "Note: input contains only chromatogram data.";
switch (config.WriteConfig.format)
{
case MSDataFile.Format.Format_MZ5:
case MSDataFile.Format.Format_mzML:
break;
default:
msg += " The selected output format can only represent spectra. Consider using mzML instead.";
break;
}
}
else
{
msg = "Note: input contains no spectra or chromatogram data.";
}
if (LogUpdate != null)
{
LogUpdate(msg, _info);
}
if (StatusUpdate != null)
{
StatusUpdate(msg, ProgressBarStyle.Continuous, _info);
}
}
if (StatusUpdate != null && msd.run.spectrumList != null)
{
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
}
// write out the new data file
var ilr = new IterationListenerRegistry();
ilr.addListener(this, 100);
msg = String.Format("Writing \"{0}\"...", outputFilename);
if (LogUpdate != null)
{
LogUpdate(msg, _info);
}
if (StatusUpdate != null)
{
StatusUpdate(msg, ProgressBarStyle.Continuous, _info);
}
MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr);
ilr.removeListener(this);
}
}
}
private void embedAllButton_Click(object sender, EventArgs e)
{
var searchPath = new StringBuilder(searchPathTextBox.Text);
string extensions = extensionsTextBox.Text;
Application.UseWaitCursor = true;
deleteAllButton.Enabled = embedAllButton.Enabled = false;
embeddedChanges = true;
try
{
// add location of original idpDBs to the search path
var mergedFilepaths = session.CreateSQLQuery("SELECT DISTINCT Filepath FROM MergedFiles").List <string>();
foreach (var filepath in mergedFilepaths)
{
searchPath.AppendFormat(";{0}", System.IO.Path.GetDirectoryName(filepath));
}
}
catch
{
// ignore if MergedFiles does not exist
}
var quantitationMethodBySource = new Dictionary <int, Embedder.QuantitationConfiguration>();
var xicConfigBySource = new Dictionary <int, Embedder.XICConfiguration> {
{ 0, _defaultXicConfig }
};
foreach (DataGridViewRow row in dataGridView.Rows)
{
int id = (int)row.Cells[idColumn.Index].Value;
var method = QuantitationMethodForRow(row.Index);
if (IsLabelFree(method))
{
xicConfigBySource[id] = (Embedder.XICConfiguration)row.Cells[quantitationSettingsColumn.Index].Value;
quantitationMethodBySource[id] = new Embedder.QuantitationConfiguration(QuantitationMethod.LabelFree, _defaultIsobaricConfig.ToString());
}
else if (IsIsobaric(method))
{
quantitationMethodBySource[id] = (Embedder.QuantitationConfiguration)row.Cells[quantitationSettingsColumn.Index].Value;
}
}
okButton.Text = "Cancel";
EmbedInProgress = true;
new Thread(() =>
{
try
{
var ilr = new IterationListenerRegistry();
ilr.addListener(new EmbedderIterationListener(this), 1);
var tempFolder = string.Empty;
var splitSourceList = new List <List <string> >();
if (quantitationMethodBySource.Any(x => IsLabelFree(x.Value.QuantitationMethod)) && xicConfigBySource.Any(x => x.Value.AlignRetentionTime))
{
tempFolder = getTempFolder();
splitSourceList = GetRTAlignGroups();
}
string idpDbFilepath = session.Connection.GetDataSource();
if (embedScanTimeOnlyBox.Checked)
{
Embedder.EmbedScanTime(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, ilr);
}
else
{
Embedder.Embed(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, ilr);
}
if (quantitationMethodBySource.Any(x => IsLabelFree(x.Value.QuantitationMethod)))
{
BeginInvoke(new MethodInvoker(() => ModeandDefaultPanel.Visible = false));
if (xicConfigBySource.Any(x => x.Value.AlignRetentionTime))
{
try
{
RTAlignPreparations(splitSourceList, tempFolder);
foreach (var kvp in xicConfigBySource)
{
kvp.Value.RTFolder = tempFolder;
}
}
catch (Exception rtError)
{
MessageBox.Show("Error: Cannot prepare RT alignment. Skipping to next stage." +
Environment.NewLine + rtError.Message);
foreach (var kvp in xicConfigBySource)
{
kvp.Value.AlignRetentionTime = false;
}
}
}
Embedder.EmbedMS1Metrics(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, xicConfigBySource, ilr);
if (!string.IsNullOrEmpty(tempFolder) && Directory.Exists(tempFolder))
{
Directory.Delete(tempFolder, true);
}
BeginInvoke(new MethodInvoker(() => ModeandDefaultPanel.Visible = true));
}
}
catch (Exception ex)
{
if (ex.Message.Contains("QuantitationConfiguration"))
{
string message = ex.Message.Replace("[QuantitationConfiguration] ", "");
message = Char.ToUpper(message[0]) + message.Substring(1);
MessageBox.Show(message);
}
else if (ex.Message.Contains("no filepath"))
{
bool multipleMissingFilepaths = ex.Message.Contains("\n");
string missingFilepaths = ex.Message.Replace("\n", "\r\n");
missingFilepaths = missingFilepaths.Replace("[embed] no", "No");
missingFilepaths = missingFilepaths.Replace("[embedScanTime] no", "No");
MessageBox.Show(missingFilepaths + "\r\n\r\nCheck that " +
(multipleMissingFilepaths ? "these source files" : "this source file") +
" can be found in the search path with one of the specified extensions.");
}
else
{
Program.HandleException(ex);
}
}
BeginInvoke(new MethodInvoker(() => Refresh()));
}).Start();
}
void processFile(string filename, Config config, ReaderList readers, Map <string, int> usedOutputFilenames)
{
// read in data file
using (var msdList = new MSDataList())
{
string msg = String.Format("Opening file \"{0}\" for read...", filename);
var stripCredentialsMatch = Regex.Match(filename, "https?://([^:]+:[^@]+@).*", RegexOptions.CultureInvariant | RegexOptions.IgnoreCase);
if (stripCredentialsMatch.Success)
{
msg = msg.Replace(stripCredentialsMatch.Groups[1].Value, "");
}
LogUpdate?.Invoke(msg, _info);
StatusUpdate?.Invoke(msg, ProgressBarStyle.Marquee, _info);
readers.read(filename, msdList, config.ReaderConfig);
foreach (var msd in msdList)
{
try
{
var outputFilename = config.outputFilename(filename, msd);
string deduplicatedFilename = outputFilename;
StatusUpdate?.Invoke("Waiting...", ProgressBarStyle.Marquee, _info);
// only one thread
lock (_calculateSHA1Mutex)
{
// if output name is same as input name, add a suffix
if (filename == outputFilename)
{
++usedOutputFilenames[outputFilename];
}
if (usedOutputFilenames.Contains(deduplicatedFilename))
{
deduplicatedFilename = deduplicatedFilename.Replace(Path.GetExtension(outputFilename), String.Format(" ({0}).{1}", usedOutputFilenames[outputFilename] + 1, Path.GetExtension(outputFilename)));
}
++usedOutputFilenames[outputFilename];
LogUpdate?.Invoke("Calculating SHA1 checksum...", _info);
StatusUpdate?.Invoke("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
MSDataFile.calculateSHA1Checksums(msd);
}
var ilr = new IterationListenerRegistry();
ilr.addListenerWithTimer(this, 1);
LogUpdate?.Invoke("Processing...", _info);
StatusUpdate?.Invoke("Processing...", ProgressBarStyle.Marquee, _info);
SpectrumListFactory.wrap(msd, config.Filters, ilr);
config.WriteConfig.useWorkerThreads = msd.run.spectrumList.benefitsFromWorkerThreads();
if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty())
{
if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty())
{
msg = "Note: input contains only chromatogram data.";
switch (config.WriteConfig.format)
{
case MSDataFile.Format.Format_MZ5:
case MSDataFile.Format.Format_mzML:
break;
default:
msg += " The selected output format can only represent spectra. Consider using mzML instead.";
break;
}
}
else
{
msg = "Note: input contains no spectra or chromatogram data.";
}
LogUpdate?.Invoke(msg, _info);
StatusUpdate?.Invoke(msg, ProgressBarStyle.Continuous, _info);
}
if (StatusUpdate != null && msd.run.spectrumList != null)
{
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
}
// write out the new data file
msg = String.Format("Writing \"{0}\"...", deduplicatedFilename);
LogUpdate?.Invoke(msg, _info);
StatusUpdate?.Invoke(msg, ProgressBarStyle.Continuous, _info);
MSDataFile.write(msd, deduplicatedFilename, config.WriteConfig, ilr);
ilr.removeListener(this);
}
finally
{
msd.Dispose();
}
}
}
}
private void embedAllButton_Click (object sender, EventArgs e)
{
var searchPath = new StringBuilder(searchPathTextBox.Text);
string extensions = extensionsTextBox.Text;
Application.UseWaitCursor = true;
deleteAllButton.Enabled = embedAllButton.Enabled = false;
embeddedChanges = true;
try
{
// add location of original idpDBs to the search path
var mergedFilepaths = session.CreateSQLQuery("SELECT DISTINCT Filepath FROM MergedFiles").List<string>();
foreach (var filepath in mergedFilepaths)
searchPath.AppendFormat(";{0}", System.IO.Path.GetDirectoryName(filepath));
}
catch
{
// ignore if MergedFiles does not exist
}
var quantitationMethodBySource = new Dictionary<int, Embedder.QuantitationConfiguration>();
var xicConfigBySource = new Dictionary<int, Embedder.XICConfiguration>{{0, _defaultXicConfig}};
foreach (DataGridViewRow row in dataGridView.Rows)
{
int id = (int) row.Cells[idColumn.Index].Value;
var method = QuantitationMethodForRow(row.Index);
if (IsLabelFree(method))
{
xicConfigBySource[id] = (Embedder.XICConfiguration) row.Cells[quantitationSettingsColumn.Index].Value;
quantitationMethodBySource[id] = new Embedder.QuantitationConfiguration(QuantitationMethod.LabelFree, _defaultIsobaricConfig.ToString());
}
else if (IsIsobaric(method))
quantitationMethodBySource[id] = (Embedder.QuantitationConfiguration) row.Cells[quantitationSettingsColumn.Index].Value;
}
okButton.Text = "Cancel";
EmbedInProgress = true;
new Thread(() =>
{
try
{
var ilr = new IterationListenerRegistry();
ilr.addListener(new EmbedderIterationListener(this), 1);
var tempFolder = string.Empty;
var splitSourceList = new List<List<string>>();
if (quantitationMethodBySource.Any(x => IsLabelFree(x.Value.QuantitationMethod)) && xicConfigBySource.Any(x => x.Value.AlignRetentionTime))
{
tempFolder = getTempFolder();
splitSourceList = GetRTAlignGroups();
}
string idpDbFilepath = session.Connection.GetDataSource();
if (embedScanTimeOnlyBox.Checked)
Embedder.EmbedScanTime(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, ilr);
else
Embedder.Embed(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, ilr);
if (quantitationMethodBySource.Any(x => IsLabelFree(x.Value.QuantitationMethod)))
{
BeginInvoke(new MethodInvoker(() => ModeandDefaultPanel.Visible = false));
if (xicConfigBySource.Any(x => x.Value.AlignRetentionTime))
{
try
{
RTAlignPreparations(splitSourceList, tempFolder);
foreach (var kvp in xicConfigBySource)
kvp.Value.RTFolder = tempFolder;
}
catch (Exception rtError)
{
MessageBox.Show("Error: Cannot prepare RT alignment. Skipping to next stage." +
Environment.NewLine + rtError.Message);
foreach (var kvp in xicConfigBySource)
kvp.Value.AlignRetentionTime = false;
}
}
Embedder.EmbedMS1Metrics(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, xicConfigBySource, ilr);
if (!string.IsNullOrEmpty(tempFolder) && Directory.Exists(tempFolder))
Directory.Delete(tempFolder,true);
BeginInvoke(new MethodInvoker(() => ModeandDefaultPanel.Visible = true));
}
}
catch (Exception ex)
{
if (ex.Message.Contains("QuantitationConfiguration"))
{
string message = ex.Message.Replace("[QuantitationConfiguration] ", "");
message = Char.ToUpper(message[0]) + message.Substring(1);
MessageBox.Show(message);
}
else if (ex.Message.Contains("no filepath"))
{
bool multipleMissingFilepaths = ex.Message.Contains("\n");
string missingFilepaths = ex.Message.Replace("\n", "\r\n");
missingFilepaths = missingFilepaths.Replace("[embed] no", "No");
missingFilepaths = missingFilepaths.Replace("[embedScanTime] no", "No");
MessageBox.Show(missingFilepaths + "\r\n\r\nCheck that " +
(multipleMissingFilepaths ? "these source files" : "this source file") +
" can be found in the search path with one of the specified extensions.");
}
else
Program.HandleException(ex);
}
BeginInvoke(new MethodInvoker(() => Refresh()));
}).Start();
}
void processFile(string filename, Config config, ReaderList readers)
{
if (LogUpdate != null)
{
LogUpdate("Opening file...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Opening file...", ProgressBarStyle.Marquee, _info);
}
// read in data file
using (var msdList = new MSDataList())
{
readers.read(filename, msdList);
foreach (var msd in msdList)
{
var outputFilename = config.outputFilename(filename, msd);
if (filename == outputFilename)
{
throw new ArgumentException("Output filepath is the same as input filepath");
}
if (LogUpdate != null)
{
LogUpdate("Calculating SHA1 checksum...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
}
// only one thread
lock (calculateSHA1Mutex)
MSDataFile.calculateSHA1Checksums(msd);
if (LogUpdate != null)
{
LogUpdate("Processing...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info);
}
SpectrumListFactory.wrap(msd, config.Filters);
if (StatusUpdate != null && msd.run.spectrumList != null)
{
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
}
// write out the new data file
IterationListenerRegistry ilr = null;
ilr = new IterationListenerRegistry();
ilr.addListener(this, 100);
MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr);
}
}
}
void processFile(string filename, Config config, ReaderList readers)
{
// read in data file
using (var msdList = new MSDataList())
{
string msg = String.Format("Opening file \"{0}\" for read...",filename);
if (LogUpdate != null) LogUpdate(msg, _info);
if (StatusUpdate != null) StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
readers.read(filename, msdList);
foreach (var msd in msdList)
{
var outputFilename = config.outputFilename(filename, msd);
if (filename == outputFilename)
throw new ArgumentException("Output filepath is the same as input filepath");
if (StatusUpdate != null) StatusUpdate("Waiting...", ProgressBarStyle.Marquee, _info);
// only one thread
lock (calculateSHA1Mutex)
{
if (LogUpdate != null) LogUpdate("Calculating SHA1 checksum...", _info);
if (StatusUpdate != null) StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
MSDataFile.calculateSHA1Checksums(msd);
}
if (LogUpdate != null) LogUpdate("Processing...", _info);
if (StatusUpdate != null) StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info);
SpectrumListFactory.wrap(msd, config.Filters);
if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty())
{
if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty())
{
msg = "Note: input contains only chromatogram data.";
switch (config.WriteConfig.format)
{
case MSDataFile.Format.Format_MZ5:
case MSDataFile.Format.Format_mzML:
break;
default:
msg += " The selected output format can only represent spectra. Consider using mzML instead.";
break;
}
}
else
msg = "Note: input contains no spectra or chromatogram data.";
if (LogUpdate != null) LogUpdate(msg, _info);
if (StatusUpdate != null) StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
}
if (StatusUpdate != null && msd.run.spectrumList != null)
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
// write out the new data file
var ilr = new IterationListenerRegistry();
ilr.addListener(this, 100);
msg = String.Format("Writing \"{0}\"...", outputFilename);
if (LogUpdate != null) LogUpdate(msg, _info);
if (StatusUpdate != null) StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr);
ilr.removeListener(this);
}
}
}
private void loadRefSeqGeneMetadata()
{
#region Check for updated gene2protein database and download it
if (!File.Exists(Path.Combine(Application.StartupPath, "gene2protein.db3")))
throw new Exception("missing gene2protein.db3 mapping file");
/*string g2pTimestamp = null;
string g2pPath = Path.Combine(Application.UserAppDataPath, "gene2protein.db3");
string g2pPathAlternate = Path.Combine(Application.StartupPath, "gene2protein.db3");
var copyUserToAlternate = new ProcessStartInfo("cmd.exe", String.Format("/C copy /Y \"{0}\" \"{1}\"", g2pPath, g2pPathAlternate));
copyUserToAlternate.CreateNoWindow = true;
if (!File.Exists(g2pPath) && File.Exists(g2pPathAlternate))
File.Copy(g2pPathAlternate, g2pPath);
else if (File.Exists(g2pPath) && !File.Exists(g2pPathAlternate))
{
var p = Process.Start(copyUserToAlternate);
p.WaitForExit();
if (p.ExitCode == 1)
MessageBox.Show("Unable to copy gene2protein.db3 from user-specific path to application path:\r\n" +
Path.GetDirectoryName(g2pPath) +
"\r\nto\r\n" +
Path.GetDirectoryName(g2pPathAlternate),
"Unable to copy");
}
if (File.Exists(g2pPath))
{
// if the file exists, check its timestamp and compare it to the timestamp on the server
using (var con = new SQLiteConnection(@"Data Source=" + g2pPath + ";Version=3"))
{
try
{
con.Open();
g2pTimestamp = con.ExecuteQuery("SELECT Timestamp FROM About").Single().GetString(0);
}
catch (Exception e)
{
throw new Exception("error getting timestamp of current gene2protein database (\"" + g2pPath + "\"): " + e.Message, e);
}
}
string g2pURL = "http://fenchurch.mc.vanderbilt.edu/bin/g2p";
string g2pTimestampURL = String.Format("{0}/G2P_TIMESTAMP", g2pURL);
string latestTimestamp;
lock (Program.WebClient)
{
latestTimestamp = Program.WebClient.DownloadString(g2pTimestampURL).Trim();
}
if (g2pTimestamp.CompareTo(latestTimestamp) < 0)
{
Invoke(new MethodInvoker(() =>
{
var form = new NewVersionForm("RefSeq Gene to Protein Database",
g2pTimestamp,
latestTimestamp,
String.Empty)
{
Owner = this,
StartPosition = FormStartPosition.CenterParent
};
if (form.ShowDialog() == DialogResult.Yes)
{
var oldG2Ptime = File.GetLastWriteTimeUtc(g2pPath);
string backupG2Pname = String.Format("{0}.{1}.bak", g2pPath, oldG2Ptime.ToString("yyyyMMddHHmm"));
try
{
if (!File.Exists(backupG2Pname))
File.Copy(g2pPath, backupG2Pname);
File.Delete(g2pPath);
string g2pDatabaseURL = String.Format("{0}/gene2protein.db3", g2pURL);
lock (Program.WebClient)
{
Program.WebClient.DownloadFile(g2pDatabaseURL, g2pPath);
var p = Process.Start(copyUserToAlternate);
p.WaitForExit();
if (p.ExitCode == 1)
MessageBox.Show("Unable to copy gene2protein.db3 from user-specific path to application path:\r\n" +
Path.GetDirectoryName(g2pPath) +
"\r\nto\r\n" +
Path.GetDirectoryName(g2pPathAlternate),
"Unable to copy");
}
g2pTimestamp = latestTimestamp;
}
catch (Exception)
{
if (!File.Exists(g2pPath))
File.Move(backupG2Pname, g2pPath);
}
}
else
g2pTimestamp = null; // no update
}));
}
else
g2pTimestamp = null; // no update
}
else // downloading database for the first time (or it has been deleted)
{
string g2pURL = "http://fenchurch.mc.vanderbilt.edu/bin/g2p";
string g2pDatabaseURL = String.Format("{0}/gene2protein.db3", g2pURL);
lock (Program.WebClient)
{
Program.WebClient.DownloadFile(g2pDatabaseURL, g2pPath);
var p = Process.Start(copyUserToAlternate);
p.WaitForExit();
if (p.ExitCode == 1)
MessageBox.Show("Unable to copy gene2protein.db3 from user-specific path to application path:\r\n" +
Path.GetDirectoryName(g2pPath) +
"\r\nto\r\n" +
Path.GetDirectoryName(g2pPathAlternate),
"Unable to copy");
}
}*/
#endregion
if (session == null)
return;
try
{
clearSession();
var ilr = new IterationListenerRegistry();
ilr.addListener(progressMonitor.GetIterationListenerProxy(), 1);
Embedder.EmbedGeneMetadata(Text, ilr);
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "embedding gene metadata failed");
}
OpenFiles(new List<string> { Text }, null);
}
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 ProgressForm(IEnumerable<string> taskNames, IterationListenerRegistry ilr)
{
InitializeComponent();
_progressCellByTaskName = new Dictionary<string, DataGridViewProgressCell>();
_textBoxLogByTaskName = new Dictionary<string, TextBox>();
_lastMessageByTaskName = new Dictionary<string, string>();
_rowByTaskName = new Dictionary<string, DataGridViewRow>();
_tasksDone = 0;
_ilr = ilr;
_ilProxy = new IterationListenerProxy() { form = this };
_ilr.addListener(_ilProxy, 1000);
var boxShown = false;
foreach (var task in taskNames)
{
var textBox = _textBoxLogByTaskName[task] = new TextBox
{
Text = String.Format("{0}{1}{0}Starting...{0}",
Environment.NewLine,
new string('-', 30)),
Dock = DockStyle.Fill,
Multiline = true,
ScrollBars = ScrollBars.Vertical
};
if (boxShown)
textBox.Visible = false;
else
{
textBox.Visible = true;
boxShown = true;
}
ProgressSplit.Panel2.Controls.Add(textBox);
JobDataView.Rows.Add(task, 0);
var row = JobDataView.Rows[JobDataView.Rows.Count - 1];
row.Tag = textBox;
_rowByTaskName[task] = row;
_progressCellByTaskName[task] = row.Cells[1] as DataGridViewProgressCell;
_progressCellByTaskName[task].Text = "waiting";
}
}
