public ConfigWizard(HistoryItem hi, IList<ConfigFile> templateList, bool editMode)
{
InitializeComponent();
_currentJob = hi;
_templateList = templateList;
_editMode = editMode;
if (editMode)
Text = "Edit Job";
}
/// <summary>
/// Dialogue used to create new job. Fields pre-filled and appearance changed to edit mode if true
/// </summary>
/// <param name="oldFiles">List of used HistoryItems</param>
/// <param name="hi">History Item to clone from</param>
/// <param name="editMode">True if form should visually appear to be an edit box</param>
/// <param name="templates">List of available templates</param>
public AddJobForm(HistoryItem hi, IList<ConfigFile> templates, bool editMode, Form parentForm)
{
InitializeComponent();
SearchTypeBox.Text = JobType.Myrimatch;
SetHistoryItem(hi);
if (editMode)
{
Text = "Edit Job";
AddJobRunButton.Text = "Save";
}
_templateList = templates;
_parentForm = parentForm;
}
/// <summary>
/// Starts Bumbershoot utility based on current row and destination program
/// </summary>
private void ProcessJob(HistoryItem hi)
{
var argumentString = new StringBuilder();
string configString;
_killed = false;
ProcessStartInfo psi;
if (hi.Cpus > 0 && (_destinationProgram != "Comet" && _destinationProgram != "MSGF"))
argumentString.Append(string.Format("-cpus {0} ", hi.Cpus));
var workingDirectory = hi.OutputDirectory.TrimEnd('*');
switch (_destinationProgram)
{
case "MyriMatch":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\MyriMatch\myrimatch.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
configString = hi.InitialConfigFile.FilePath == "--Custom--"
? PropertyListToOverrideString(hi.InitialConfigFile.PropertyList)
: string.Format("-cfg \"{0}\" ", hi.InitialConfigFile.FilePath);
//continue to set up argument string
argumentString.Append(String.Format("{0}-ProteinDatabase \"{1}\"",
configString,
hi.ProteinDatabase));
//add files to scan to argument string
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
}
else
foreach (var file in hi.FileList)
{
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
break;
case "Comet":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\comet.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//create temp params file
var cometConfig = new List<ConfigProperty>(hi.InitialConfigFile.PropertyList).Find(x => x.Name == "config");
if (cometConfig == null)
{
JobFinished(false, true);
return;
}
var tempCometPath = Path.GetTempFileName();
_tempFiles.Add(tempCometPath);
var tempCometParams = new StreamWriter(tempCometPath);
tempCometParams.Write(cometConfig.Value);
tempCometParams.Flush();
tempCometParams.Close();
//make sure fasta has no spaces in name
var cometDB = hi.ProteinDatabase;
if (cometDB.Contains(" "))
{
cometDB = Path.GetTempFileName();
File.Copy(hi.ProteinDatabase, cometDB,true);
_tempFiles.Add(cometDB);
}
argumentString.Append(" -P\"" + tempCometPath + "\"");
argumentString.Append(" -D\"" + cometDB + "\"");
//add files to scan to argument string
_moveFileList = new List<string>();
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
foreach (var file in maskedFiles)
{
var noExtension = Path.Combine(initialDir,
Path.GetFileNameWithoutExtension(file) ?? string.Empty);
var cometParams = CometHandler.FileContentsToCometParams(cometConfig.Value);
_moveFileList.Add(noExtension + cometParams.OutputSuffix + ".pep.xml");
}
}
else
{
foreach (var file in hi.FileList)
{
var initialDir = Path.GetDirectoryName(hi.FileList[0].FilePath.Trim('"').Trim('!'));
var noExtension = Path.Combine(initialDir ?? string.Empty,
Path.GetFileNameWithoutExtension(file.FilePath.Trim('"')) ?? string.Empty);
var cometParams = CometHandler.FileContentsToCometParams(cometConfig.Value);
_moveFileList.Add(noExtension + cometParams.OutputSuffix + ".pep.xml");
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
}
break;
case "MSGF":
//find java path
var javaPath = string.Empty;
string environmentPath = Environment.GetEnvironmentVariable("JAVA_HOME");
if (!string.IsNullOrEmpty(environmentPath))
javaPath = environmentPath;
else
{
var javaKey = "SOFTWARE\\JavaSoft\\Java Runtime Environment\\";
var rk = Microsoft.Win32.Registry.LocalMachine.OpenSubKey(javaKey);
if (rk != null)
{
string currentVersion = rk.GetValue("CurrentVersion").ToString();
using (Microsoft.Win32.RegistryKey key = rk.OpenSubKey(currentVersion))
javaPath = key.GetValue("JavaHome").ToString();
}
else
{
javaKey = "SOFTWARE\\JavaSoft\\Java Development Kit\\";
rk = Microsoft.Win32.Registry.LocalMachine.OpenSubKey(javaKey);
if (rk != null)
{
string currentVersion = rk.GetValue("CurrentVersion").ToString();
using (Microsoft.Win32.RegistryKey key = rk.OpenSubKey(currentVersion))
javaPath = key.GetValue("JavaHome").ToString();
}
}
}
if (javaPath == string.Empty)
throw new Exception("Could not locate Java path");
//Set location of the program
psi = new ProcessStartInfo(Path.Combine(javaPath, "bin\\java.exe"));
if (_msgfList == null || _msgfList.Count == 0)
{
//create temp mods file
var msgfOverload = new List<ConfigProperty>(hi.InitialConfigFile.PropertyList).Find(x => x.Name == "config");
var msgfMods = new List<ConfigProperty>(hi.InitialConfigFile.PropertyList).Find(x => x.Name == "mods");
if (msgfOverload == null || msgfMods == null)
{
JobFinished(false, true);
return;
}
var tempMSGFPath = Path.GetTempFileName();
_tempFiles.Add(tempMSGFPath);
var tempMSGFMods = new StreamWriter(tempMSGFPath);
tempMSGFMods.Write(msgfMods.Value);
tempMSGFMods.Flush();
tempMSGFMods.Close();
//set up file list
var fileList = new List<string>();
_moveFileList = new List<string>();
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
fileList.AddRange(maskedFiles.Select(file => "\"" + file + "\""));
foreach (var file in maskedFiles)
{
var noExtension = Path.Combine(initialDir,
Path.GetFileNameWithoutExtension(file) ?? string.Empty);
var msgfParams = MSGFHandler.OverloadToMSGFParams(msgfOverload.Value);
_moveFileList.Add(noExtension + msgfParams.OutputSuffix + ".mzid");
}
}
else
{
fileList.AddRange(hi.FileList.Select(file => file.FilePath));
foreach (var file in hi.FileList)
{
var initialDir = Path.GetDirectoryName(hi.FileList[0].FilePath.Trim('"').Trim('!'));
var noExtension = Path.Combine(initialDir,
Path.GetFileNameWithoutExtension(file.FilePath.Trim('"')) ?? string.Empty);
var msgfParams = MSGFHandler.OverloadToMSGFParams(msgfOverload.Value);
_moveFileList.Add(noExtension + msgfParams.OutputSuffix + ".mzid");
}
}
_filesToProcess = fileList.Count;
//create overload List
_msgfList = new List<string>();
foreach (var file in fileList)
{
var arg = new StringBuilder();
arg.AppendFormat(@"-d64 -Xmx4000M -jar ""{0}\lib\MSGFPlus.jar""", AppDomain.CurrentDomain.BaseDirectory);
arg.Append(" -d \"" + hi.ProteinDatabase + "\"");
arg.Append(" -mod \"" + tempMSGFPath + "\"");
var noExtension = Path.Combine(Path.GetDirectoryName(file.Trim('"')) ?? string.Empty,
Path.GetFileNameWithoutExtension(file.Trim('"')) ?? string.Empty);
arg.Append(" " + msgfOverload.Value.Trim()
.Replace("[FileNameOnly]", noExtension)
.Replace("[FullFileName]", file.Trim('"')));
_msgfList.Add(arg.ToString());
}
}
if (_fileProcessing >= 0 || _fileProcessing < _msgfList.Count)
argumentString.Append(_msgfList[_fileProcessing]);
else
JobFinished(false, true);
_fileProcessing++;
break;
case "DirecTag":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\DirecTag\directag.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
configString = hi.InitialConfigFile.FilePath == "--Custom--"
? PropertyListToOverrideString(hi.InitialConfigFile.PropertyList)
: string.Format("-cfg \"{0}\" ", hi.InitialConfigFile.FilePath);
//HACK: Remove when deisotoping is usable
configString += string.Format("-{0} {1} ", "DeisotopingMode", "0");
//continue to set up argument string
argumentString.Append(configString.Trim());
//add files to scan to argument string
_direcTagMask = null;
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
_direcTagMask = fullMask;
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
}
else
foreach (var file in hi.FileList)
{
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
break;
case "TagRecon":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\TagRecon\tagrecon.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
if (hi.TagConfigFile.FilePath == "--Custom--")
{
configString = PropertyListToOverrideString(hi.TagConfigFile.PropertyList);
//use intranal blosum and unimod files if not specified
if (!configString.Contains("-Blosum "))
configString += string.Format("-{0} \"{1}\" ", "Blosum",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\blosum62.fas"));
if (!configString.Contains("UnimodXML"))
configString += string.Format("-{0} \"{1}\" ", "UnimodXML",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\unimod.xml"));
}
else
{
configString = string.Format("-cfg \"{0}\" ", hi.TagConfigFile.FilePath);
var configCheck = new StreamReader(hi.TagConfigFile.FilePath);
var entireFile = configCheck.ReadToEnd();
configCheck.Close();
if (!entireFile.Contains("Blosum ="))
configString += string.Format("-{0} \"{1}\" ", "Blosum",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\blosum62.fas"));
if (!entireFile.Contains("UnimodXML ="))
configString += string.Format("-{0} \"{1}\" ", "UnimodXML",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\unimod.xml"));
}
//continue to set up argument string
argumentString.Append(String.Format("{0}-ProteinDatabase \"{1}\"",
configString,
hi.ProteinDatabase));
//add files to scan to argument string
foreach (var file in _completedFiles)
{
argumentString.AppendFormat(" \"{0}\"", Path.Combine(hi.OutputDirectory.TrimEnd('*'), file));
_filesToProcess++;
}
break;
case "Pepitome":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\Pepitome\pepitome.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
configString = hi.InitialConfigFile.FilePath == "--Custom--"
? PropertyListToOverrideString(hi.InitialConfigFile.PropertyList)
: string.Format("-cfg \"{0}\" ", hi.InitialConfigFile.FilePath);
//continue to set up argument string
argumentString.Append(String.Format("{0}-ProteinDatabase \"{1}\" -SpectralLibrary \"{2}\"",
configString, hi.ProteinDatabase, hi.SpectralLibrary));
//add files to scan to argument string
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
}
else
foreach (var file in hi.FileList)
{
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
break;
default:
//should never be called, throw error if it is
throw new Exception(String.Format("Destination Program not set to known value: {0}",
_destinationProgram));
}
psi.WorkingDirectory = workingDirectory;
psi.Arguments = argumentString.ToString();
var commandGiven = (string.Format("Command given:{0}{1}>{2} {3}{0}{0}", Environment.NewLine, psi.WorkingDirectory, psi.FileName, psi.Arguments));
SendToLog(commandGiven);
//Make sure window stays hidden
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
psi.UseShellExecute = false;
psi.CreateNoWindow = true;
_runningProgram = new Process
{
StartInfo = psi,
EnableRaisingEvents = true
};
_runningProgram.Start();
_runningProgram.PriorityClass = ProcessPriorityClass.BelowNormal;
_runningProgram.BeginOutputReadLine();
_runningProgram.OutputDataReceived += DataReceived;
_runningProgram.BeginErrorReadLine();
_runningProgram.ErrorDataReceived += ErrorCaught;
_runningProgram.Exited += (x, y) =>
{
var bgWait = new BackgroundWorker();
bgWait.DoWork += (zzz, e) =>
{
SendToLog(" ---Program exit detected---");
Thread.Sleep(100);
SendToLog(" ---Calculating results---");
var a = ((object[])e.Argument)[0];
var b = (EventArgs)((object[])e.Argument)[1];
ProgramExited(a, b);
};
bgWait.RunWorkerAsync(new object[] { x, y });
//ProgramExited(x,y);
};
}
/// <summary>
/// Selects the destination program and sets it to run in the background
/// </summary>
/// <param name="rowNumber"></param>
/// <param name="hi"></param>
internal void StartNewJob(int rowNumber, HistoryItem hi)
{
_scanning = true;
_versionCaught = false;
_currentRow = rowNumber;
_minPercentage = 0;
_fileProcessing = 0;
_filesToProcess = 0;
_tempFiles = new List<string>();
_currentHI = hi;
ThreadStart ts = () => ProcessJob(hi);
_workThread = new Thread(ts)
{
Name = "Program Handler",
IsBackground = true
};
if (hi.JobType == JobType.Myrimatch)
{
_completedFiles = new List<string>();
_destinationProgram = "MyriMatch";
SendToLog("BumberDash- Job has started");
}
else if (hi.JobType == JobType.Comet)
{
_completedFiles = new List<string>();
_destinationProgram = "Comet";
SendToLog("BumberDash- Job has started");
}
else if (hi.JobType == JobType.MSGF)
{
_completedFiles = new List<string>();
_destinationProgram = "MSGF";
SendToLog("BumberDash- Job has started");
}
else if (hi.JobType == JobType.Library)
{
_completedFiles = new List<string>();
_destinationProgram = "Pepitome";
SendToLog("BumberDash- Job has started");
}
else if (_destinationProgram == "DirecTag")
{
_destinationProgram = "TagRecon";
SendToLog(string.Format("{0}{1}{0}", Environment.NewLine, new string('-', 20)));
}
else
{
_completedFiles = new List<string>();
_destinationProgram = "DirecTag";
SendToLog("BumberDash- Job has started");
}
_workThread.Start();
}
public static ISessionFactory CreateSessionFactory()
{
var currentGuiVersion = Assembly.GetExecutingAssembly().GetName().Version.ToString(3);
var newdatabase = false;
var root = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData),"Bumberdash");
if (!Directory.Exists(root))
Directory.CreateDirectory(root);
var dataFile = Path.Combine(root, "Bumbershoot " + currentGuiVersion + ".db");
var newfactory = CreateSessionFactory(dataFile, true);
var session = newfactory.OpenSession();
//check that all preloaded templates are present
if (session.QueryOver<ConfigFile>().List().Count<16)
{
//check for presence of completely empty database
if (session.QueryOver<HistoryItem>().List().Count == 0 &&
session.QueryOver<ConfigFile>().List().Count == 0)
newdatabase = true;
//load base database
var baseRoot = Path.GetDirectoryName(Process.GetCurrentProcess().MainModule.FileName);
if (baseRoot == null)
throw new Exception("Cannot find base database file");
if (!File.Exists(Path.Combine(baseRoot, "lib\\Bumbershoot.db")))
throw new Exception("Looking for \"" + Path.Combine(baseRoot, "lib\\Bumbershoot.db") + "\", however I cant find it");
var baseFactory = CreateSessionFactory(Path.Combine(baseRoot, "lib\\Bumbershoot.db"), false);
var baseSession = baseFactory.OpenSession();
//load base templates
var connectedBaseConfigs = baseSession.QueryOver<ConfigFile>().List();
var baseConfigs = new List<ConfigFile>();
foreach (var config in connectedBaseConfigs)
{
var newInstrument = new ConfigFile
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath,
PropertyList = new List<ConfigProperty>()
};
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
newInstrument.PropertyList.Add(newProperty);
}
baseConfigs.Add(newInstrument);
}
//delete old templates (if any remain) and load base template
foreach (var config in baseConfigs)
{
ConfigFile config1 = config;
var deleteList = session.QueryOver<ConfigFile>()
.Where(x => x.Name == config1.Name &&
x.DestinationProgram == config1.DestinationProgram)
.List();
foreach (var item in deleteList)
session.Delete(item);
session.Flush();
var newInstrument = new ConfigFile()
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath
};
session.SaveOrUpdate(newInstrument);
session.Flush();
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty()
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
}
//automatically try to recover old history items if database is flagged as new
if (newdatabase)
{
//if database structure is ever changed this will need to be updated to include conversion (probably in the form of basic sqlite queries)
var directoryInfo = new DirectoryInfo(root);
var bdFiles = directoryInfo.GetFiles("Bumbershoot*.db").Select(file => file.Name).ToList();
bdFiles.Sort();
if (bdFiles.Count > 1)
{
//reorder to proper location
if (bdFiles[bdFiles.Count - 1] == "Bumbershoot.db")
{
bdFiles.RemoveAt(bdFiles.Count - 1);
bdFiles.Insert(0, "Bumbershoot.db");
}
var restorePath = Path.Combine(root, bdFiles[bdFiles.Count - 2]);
var restoreFactory = CreateSessionFactory(restorePath, true);
var restoreSession = restoreFactory.OpenSession();
var restoreJobs = restoreSession.QueryOver<HistoryItem>().List<HistoryItem>();
var restoredConfigs = new Dictionary<int,ConfigFile>();
//start restoring jobs
foreach (var job in restoreJobs)
{
var newjob = new HistoryItem
{
Cpus = job.Cpus, CurrentStatus = job.CurrentStatus,
EndTime = job.EndTime, JobName = job.JobName,
JobType = job.JobType, OutputDirectory = job.OutputDirectory,
ProteinDatabase = job.ProteinDatabase, RowNumber = job.RowNumber,
SpectralLibrary = job.SpectralLibrary, StartTime = job.StartTime
};
if (!restoredConfigs.ContainsKey(job.InitialConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.InitialConfigFile.DestinationProgram,
FilePath = job.InitialConfigFile.FilePath,
FirstUsedDate = job.InitialConfigFile.FirstUsedDate,
Name = job.InitialConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.InitialConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.InitialConfigFile = newConfig;
restoredConfigs.Add(job.InitialConfigFile.ConfigId, newConfig);
}
else
newjob.InitialConfigFile = restoredConfigs[job.InitialConfigFile.ConfigId];
if (job.TagConfigFile != null)
{
if (!restoredConfigs.ContainsKey(job.TagConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.TagConfigFile.DestinationProgram,
FilePath = job.TagConfigFile.FilePath,
FirstUsedDate = job.TagConfigFile.FirstUsedDate,
Name = job.TagConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.TagConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.TagConfigFile = newConfig;
restoredConfigs.Add(job.TagConfigFile.ConfigId,newConfig);
}
else
newjob.TagConfigFile = restoredConfigs[job.TagConfigFile.ConfigId];
}
session.SaveOrUpdate(newjob);
session.Flush();
foreach (var file in job.FileList)
{
var newFile = new InputFile {FilePath = file.FilePath, HistoryItem = newjob};
session.SaveOrUpdate(newFile);
session.Flush();
}
}
}
}
}
session.Close();
return newfactory;
}
public List<HistoryItem> GetHistoryItems()
{
var hiList = new List<HistoryItem>();
var files = GetInputFileNames();
var outputDir = OutputDirectoryBox.Text;
//generic hi setup
var initialHi = new HistoryItem
{
JobName = NameBox.Text,
OutputDirectory = newFolderBox.Checked ? outputDir + "+" : outputDir,
ProteinDatabase = DatabaseLocBox.Text,
Cpus = 0,
CurrentStatus = string.Empty,
StartTime = null,
EndTime = null,
RowNumber = 0,
TagConfigFile = null,
FileList = new List<InputFile>()
};
foreach (var item in files)
initialHi.FileList.Add(new InputFile { FilePath = item, HistoryItem = initialHi });
if (SearchTypeBox.Text == JobType.Library)
{
initialHi.JobType = JobType.Library;
initialHi.SpectralLibrary = SpecLibBox.Text;
initialHi.InitialConfigFile = GetConfigFile("Pepitome");
//HACK: Until fix gets pushed out Pepitome should only run with 1 cpu core
initialHi.Cpus = 1;
}
else if (SearchTypeBox.Text == JobType.Tag)
{
initialHi.JobType = JobType.Tag;
initialHi.InitialConfigFile = GetConfigFile("DirecTag");
initialHi.TagConfigFile = GetConfigFile("TagRecon");
}
else if (SearchTypeBox.Text == JobType.Myrimatch)
{
var newOutput = initialHi.OutputDirectory;
initialHi.JobType = JobType.Myrimatch;
initialHi.InitialConfigFile = GetConfigFile("MyriMatch");
if (MyriActiveBox.Checked && newFolderBox.Checked)
newOutput = Path.Combine(outputDir ?? string.Empty, NameBox.Text);
var cometHi = new HistoryItem
{
JobType = JobType.Comet,
OutputDirectory = newOutput,
JobName = initialHi.JobName,
ProteinDatabase = initialHi.ProteinDatabase,
Cpus = 0,
CurrentStatus = string.Empty,
StartTime = null,
EndTime = null,
RowNumber = 0,
InitialConfigFile = GetConfigFile("Comet"),
FileList = new List<InputFile>()
};
var msgfHi = new HistoryItem
{
JobType = JobType.MSGF,
OutputDirectory = newOutput,
JobName = initialHi.JobName,
ProteinDatabase = initialHi.ProteinDatabase,
Cpus = 0,
CurrentStatus = string.Empty,
StartTime = null,
EndTime = null,
RowNumber = 0,
InitialConfigFile = GetConfigFile("MSGF"),
FileList = new List<InputFile>()
};
foreach (var item in files)
{
cometHi.FileList.Add(new InputFile { FilePath = item, HistoryItem = cometHi });
msgfHi.FileList.Add(new InputFile { FilePath = item, HistoryItem = msgfHi });
}
if (CometActiveBox.Checked)
hiList.Add(cometHi);
if (MSGFActiveBox.Checked)
hiList.Add(msgfHi);
}
else
throw new Exception("None of the known search types were checked." +
" Was there a new one added that hasn't been accounted for?");
if (SearchTypeBox.Text != JobType.Myrimatch || MyriActiveBox.Checked)
hiList.Insert(0, initialHi);
return hiList;
}
/// <summary>
/// Returns new history item from form
/// </summary>
/// <returns></returns>
internal HistoryItem GetHistoryItem()
{
var hi = new HistoryItem
{
JobName = NameBox.Text,
JobType = SearchTypeBox.Text,
OutputDirectory = OutputDirectoryBox.Text +
(newFolderBox.Checked ? "+" : string.Empty),
ProteinDatabase = DatabaseLocBox.Text,
SpectralLibrary = SearchTypeBox.Text == JobType.Library
? SpecLibBox.Text
: null,
Cpus = (int) CPUsBox.Value,
CurrentStatus = string.Empty,
StartTime = null,
EndTime = null,
RowNumber = 0,
InitialConfigFile = GetConfigFile(
SearchTypeBox.Text == JobType.Myrimatch
? "MyriMatch"
: (SearchTypeBox.Text == JobType.Tag
? "DirecTag"
: "Pepitome")),
TagConfigFile = SearchTypeBox.Text == JobType.Tag
? GetConfigFile("TagRecon")
: null
};
//File List
if (hi.FileList == null)
hi.FileList = new List<InputFile>();
else
hi.FileList.Clear();
var files = GetInputFileNames();
foreach (var item in files)
hi.FileList.Add(new InputFile { FilePath = item, HistoryItem = hi });
return hi;
}
/// <summary>
/// Populates fields with recieved values
/// </summary>
/// <param name="hi"></param>
private void SetHistoryItem(HistoryItem hi)
{
var fileList = hi.FileList.Select(file => file.FilePath).Distinct().ToList();
NameBox.Text = hi.JobName;
CPUsBox.Value = hi.Cpus;
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
InputMethodBox.Text = "File Mask";
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
InputDirectoryBox.Text = initialDir;
FileMaskBox.Text = mask;
}
else
{
InputMethodBox.Text = "File List";
var usedFiles = GetInputFileNames();
foreach (var file in fileList)
{
if (usedFiles.Contains(file))
continue;
var currentRow = InputFilesList.Rows.Count;
var newItem = new[] { Path.GetFileName(file.Trim('"')) };
InputFilesList.Rows.Insert(currentRow, newItem);
InputFilesList.Rows[currentRow].Cells[0].ToolTipText = file;
}
}
DatabaseLocBox.Text = hi.ProteinDatabase;
//Output directory handled differently depending on if new folder is/was created
if (hi.OutputDirectory.EndsWith("+"))
{
//folder has not been made yet, just indicate it is to be made
newFolderBox.Checked = true;
OutputDirectoryBox.Text = hi.OutputDirectory.TrimEnd('+');
}
else if (hi.OutputDirectory.EndsWith("*"))
{
//Folder has already been made, trim created folder and indicate new folder is to be made
var baseDirectory = new DirectoryInfo(hi.OutputDirectory.TrimEnd('*'));
newFolderBox.Checked = true;
OutputDirectoryBox.Text = baseDirectory.Parent != null
? baseDirectory.Parent.FullName
: hi.OutputDirectory.TrimEnd('*');
}
else
{
newFolderBox.Checked = false;
OutputDirectoryBox.Text = hi.OutputDirectory;
}
if (hi.JobType == JobType.Tag || (hi.JobType == null && hi.TagConfigFile != null))
{
if (hi.InitialConfigFile.Name == null)
DTConfigBox.Text = hi.InitialConfigFile.FilePath;
else
{
DTConfigBox.Tag = "--Custom--";
DTConfigBox.Text = hi.InitialConfigFile.Name;
}
DirecTagInfoBox.Clear();
foreach (var property in hi.InitialConfigFile.PropertyList)
DirecTagInfoBox.Text += string.Format("{0} = {1}{2}", property.Name, property.Value, Environment.NewLine);
if (hi.TagConfigFile.Name == null)
TRConfigBox.Text = hi.TagConfigFile.FilePath;
else
{
TRConfigBox.Tag = "--Custom--";
TRConfigBox.Text = hi.TagConfigFile.Name;
}
TagReconInfoBox.Clear();
foreach (var property in hi.TagConfigFile.PropertyList)
TagReconInfoBox.Text += string.Format("{0} = {1}{2}", property.Name, property.Value, Environment.NewLine);
SearchTypeBox.Text = JobType.Tag;
}
else if (hi.JobType == JobType.Library || (hi.JobType == null && hi.SpectralLibrary != null))
{
SpecLibBox.Text = hi.SpectralLibrary;
if (hi.InitialConfigFile.Name == null)
PepConfigBox.Text = hi.InitialConfigFile.FilePath;
else
{
PepConfigBox.Tag = "--Custom--";
PepConfigBox.Text = hi.InitialConfigFile.Name;
}
PepitomeInfoBox.Clear();
foreach (var property in hi.InitialConfigFile.PropertyList)
PepitomeInfoBox.Text += string.Format("{0} = {1}{2}", property.Name, property.Value, Environment.NewLine);
SearchTypeBox.Text = JobType.Library;
}
else
{
if (hi.InitialConfigFile.Name == null)
MyriConfigBox.Text = hi.InitialConfigFile.FilePath;
else
{
MyriConfigBox.Tag = "--Custom--";
MyriConfigBox.Text = hi.InitialConfigFile.Name;
}
MyriMatchInfoBox.Clear();
foreach (var property in hi.InitialConfigFile.PropertyList)
MyriMatchInfoBox.Text += string.Format("{0} = {1}{2}", property.Name, property.Value, Environment.NewLine);
SearchTypeBox.Text = JobType.Myrimatch;
}
}
public static ISessionFactory CreateSessionFactory()
{
var currentGuiVersion = Assembly.GetExecutingAssembly().GetName().Version.ToString(3);
var newdatabase = false;
var root = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData), "Bumberdash");
if (!Directory.Exists(root))
{
Directory.CreateDirectory(root);
}
var dataFile = Path.Combine(root, "Bumbershoot " + currentGuiVersion + ".db");
var newfactory = CreateSessionFactory(dataFile, true);
var session = newfactory.OpenSession();
//check that all preloaded templates are present
if (session.QueryOver <ConfigFile>().List().Count < 16)
{
//check for presence of completely empty database
if (session.QueryOver <HistoryItem>().List().Count == 0 &&
session.QueryOver <ConfigFile>().List().Count == 0)
{
newdatabase = true;
}
//load base database
var baseRoot = Path.GetDirectoryName(Process.GetCurrentProcess().MainModule.FileName);
if (baseRoot == null)
{
throw new Exception("Cannot find base database file");
}
if (!File.Exists(Path.Combine(baseRoot, "lib\\Bumbershoot.db")))
{
throw new Exception("Looking for \"" + Path.Combine(baseRoot, "lib\\Bumbershoot.db") + "\", however I cant find it");
}
var baseFactory = CreateSessionFactory(Path.Combine(baseRoot, "lib\\Bumbershoot.db"), false);
var baseSession = baseFactory.OpenSession();
//load base templates
var connectedBaseConfigs = baseSession.QueryOver <ConfigFile>().List();
var baseConfigs = new List <ConfigFile>();
foreach (var config in connectedBaseConfigs)
{
var newInstrument = new ConfigFile
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath,
PropertyList = new List <ConfigProperty>()
};
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
newInstrument.PropertyList.Add(newProperty);
}
baseConfigs.Add(newInstrument);
}
//delete old templates (if any remain) and load base template
foreach (var config in baseConfigs)
{
ConfigFile config1 = config;
var deleteList = session.QueryOver <ConfigFile>()
.Where(x => x.Name == config1.Name &&
x.DestinationProgram == config1.DestinationProgram)
.List();
foreach (var item in deleteList)
{
session.Delete(item);
}
session.Flush();
var newInstrument = new ConfigFile()
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath
};
session.SaveOrUpdate(newInstrument);
session.Flush();
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty()
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
}
//automatically try to recover old history items if database is flagged as new
if (newdatabase)
{
//if database structure is ever changed this will need to be updated to include conversion (probably in the form of basic sqlite queries)
var directoryInfo = new DirectoryInfo(root);
var bdFiles = directoryInfo.GetFiles("Bumbershoot*.db").Select(file => file.Name).ToList();
bdFiles.Sort();
if (bdFiles.Count > 1)
{
//reorder to proper location
if (bdFiles[bdFiles.Count - 1] == "Bumbershoot.db")
{
bdFiles.RemoveAt(bdFiles.Count - 1);
bdFiles.Insert(0, "Bumbershoot.db");
}
var restorePath = Path.Combine(root, bdFiles[bdFiles.Count - 2]);
var restoreFactory = CreateSessionFactory(restorePath, true);
var restoreSession = restoreFactory.OpenSession();
var restoreJobs = restoreSession.QueryOver <HistoryItem>().List <HistoryItem>();
var restoredConfigs = new Dictionary <int, ConfigFile>();
//start restoring jobs
foreach (var job in restoreJobs)
{
var newjob = new HistoryItem
{
Cpus = job.Cpus, CurrentStatus = job.CurrentStatus,
EndTime = job.EndTime, JobName = job.JobName,
JobType = job.JobType, OutputDirectory = job.OutputDirectory,
ProteinDatabase = job.ProteinDatabase, RowNumber = job.RowNumber,
SpectralLibrary = job.SpectralLibrary, StartTime = job.StartTime
};
if (!restoredConfigs.ContainsKey(job.InitialConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.InitialConfigFile.DestinationProgram,
FilePath = job.InitialConfigFile.FilePath,
FirstUsedDate = job.InitialConfigFile.FirstUsedDate,
Name = job.InitialConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.InitialConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.InitialConfigFile = newConfig;
restoredConfigs.Add(job.InitialConfigFile.ConfigId, newConfig);
}
else
{
newjob.InitialConfigFile = restoredConfigs[job.InitialConfigFile.ConfigId];
}
if (job.TagConfigFile != null)
{
if (!restoredConfigs.ContainsKey(job.TagConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.TagConfigFile.DestinationProgram,
FilePath = job.TagConfigFile.FilePath,
FirstUsedDate = job.TagConfigFile.FirstUsedDate,
Name = job.TagConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.TagConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.TagConfigFile = newConfig;
restoredConfigs.Add(job.TagConfigFile.ConfigId, newConfig);
}
else
{
newjob.TagConfigFile = restoredConfigs[job.TagConfigFile.ConfigId];
}
}
session.SaveOrUpdate(newjob);
session.Flush();
foreach (var file in job.FileList)
{
var newFile = new InputFile {
FilePath = file.FilePath, HistoryItem = newjob
};
session.SaveOrUpdate(newFile);
session.Flush();
}
}
}
}
}
session.Close();
return(newfactory);
}
public void SetHistoryItem(HistoryItem recievedHi)
{
ModBox.Rows.Clear();
//set generic values first
if (!string.IsNullOrEmpty(recievedHi.JobName))
OutputNewFolderBox.Text = recievedHi.JobName;
if (!string.IsNullOrEmpty(recievedHi.ProteinDatabase))
DatabaseBox.Text = recievedHi.ProteinDatabase;
if (!string.IsNullOrEmpty(recievedHi.SpectralLibrary))
LibraryBox.Text = recievedHi.SpectralLibrary;
if (!string.IsNullOrEmpty(recievedHi.OutputDirectory))
{
if (recievedHi.OutputDirectory.EndsWith("+") || recievedHi.OutputDirectory.EndsWith("*"))
OutputNewCheckBox.Checked = true;
OutputFolderBox.Text = recievedHi.OutputDirectory.EndsWith("*")
? Path.GetDirectoryName(recievedHi.OutputDirectory.TrimEnd('*'))
: recievedHi.OutputDirectory.TrimEnd('+');
}
if (recievedHi.FileList != null)
foreach (var file in recievedHi.FileList)
{
if (file.FilePath.StartsWith("!"))
{
InputDirectoryBox.Text = Path.GetDirectoryName(file.FilePath.TrimStart('!'));
try
{
var mask = Path.GetFileName(file.FilePath.TrimStart('!'));
if (mask.ToLower().Contains(".mz5"))
mz5Radio.Checked = true;
else if (mask.ToLower().Contains(".mzml"))
mzMLRadio.Checked = true;
else if (mask.ToLower().Contains(".mzxml"))
mzXMLRadio.Checked = true;
else if (mask.ToLower().Contains(".mgf"))
mgfRadio.Checked = true;
else if (mask.ToLower().Contains(".raw"))
rawRadio.Checked = true;
else if (mask.ToLower().Contains(".d"))
dRadio.Checked = true;
}
catch
{
//ignore, let the user figure out why folder doesn't contain the right files
}
continue;
}
InputFilesList.Rows.Add(new object[]{file.FilePath});
}
if (recievedHi.JobType == JobType.Myrimatch)
{
DBRadio.Checked = true;
MyriBox.Checked = true;
}
else if (recievedHi.JobType == JobType.Comet)
{
DBRadio.Checked = true;
MyriBox.Checked = false;
CometBox.Checked = true;
}
else if (recievedHi.JobType == JobType.MSGF)
{
DBRadio.Checked = true;
MyriBox.Checked = false;
MSGFBox.Checked = true;
}
else if (recievedHi.JobType == JobType.Tag)
TagRadio.Checked = true;
else if (recievedHi.JobType == JobType.Library)
PepRadio.Checked = true;
//get program-specific parameters
var configFile = recievedHi.InitialConfigFile.PropertyList;
if (recievedHi.JobType == JobType.Tag)
configFile = recievedHi.TagConfigFile.PropertyList;
if (recievedHi.JobType == JobType.Myrimatch ||
recievedHi.JobType == JobType.Tag ||
recievedHi.JobType == JobType.Library)
{
var currentParam = configFile.FirstOrDefault(x => x.Name == "OutputSuffix");
if (currentParam != null)
{
SuffixBox.Checked = true;
PrimarySuffixBox.Text = currentParam.Value.Trim('"');
}
currentParam = configFile.FirstOrDefault(x => x.Name == "CleavageRules");
if (currentParam != null)
CleavageAgentBox.Text = currentParam.Value.Trim('"');
currentParam = configFile.FirstOrDefault(x => x.Name == "MinTerminiCleavages");
if (currentParam != null)
{
int value;
if (int.TryParse(currentParam.Value, out value))
SpecificityBox.SelectedIndex = value;
}
currentParam = configFile.FirstOrDefault(x => x.Name == "ExplainUnknownMassShiftsAs");
if (recievedHi.JobType == JobType.Tag && currentParam != null)
BlindModBox.Checked = currentParam.Value.Trim('"') == "blindptms";
//tolerances
currentParam = recievedHi.JobType == JobType.Tag ? configFile.FirstOrDefault(x => x.Name == "PrecursorMzTolerance") : configFile.FirstOrDefault(x => x.Name == "MonoPrecursorMzTolerance");
var precursor = string.Empty;
var precursorUnit = string.Empty;
if (currentParam != null)
{
double value;
if (currentParam.Value.Trim('"').EndsWith("mz")
&& double.TryParse(currentParam.Value.Trim('"').Replace("mz", string.Empty),NumberStyles.Number,CultureInfo.InvariantCulture, out value))
{
PrecursorLowRadio.Checked = true;
precursor = value.ToString();
precursorUnit = "mz";
}
else if (currentParam.Value.Trim('"').EndsWith("ppm")
&& double.TryParse(currentParam.Value.Trim('"').Replace("ppm", string.Empty), NumberStyles.Number, CultureInfo.InvariantCulture, out value))
{
if (value > 15)
PrecursorMidRadio.Checked = true;
else
PrecursorHighRadio.Checked = true;
precursor = value.ToString();
precursorUnit = "ppm";
}
}
currentParam = configFile.FirstOrDefault(x => x.Name == "FragmentMzTolerance");
if (currentParam != null)
{
double value;
if (currentParam.Value.Trim('"').EndsWith("mz")
&& double.TryParse(currentParam.Value.Trim('"').Replace("mz", string.Empty), NumberStyles.Number, CultureInfo.InvariantCulture, out value))
{
FragmentLowRadio.Checked = true;
FragmentToleranceBox.Text = value.ToString();
FragmentToleranceUnitsBox.Text = "mz";
}
else if (currentParam.Value.Trim('"').EndsWith("ppm")
&& double.TryParse(currentParam.Value.Trim('"').Replace("ppm", string.Empty), NumberStyles.Number, CultureInfo.InvariantCulture, out value))
{
if (value > 30)
FragmentMidRadio.Checked = true;
else
FragmentHighRadio.Checked = true;
FragmentToleranceBox.Text = value.ToString();
FragmentToleranceUnitsBox.Text = "ppm";
}
}
if (!string.IsNullOrEmpty(precursor))
PrecursorToleranceBox.Text = precursor;
if (!string.IsNullOrEmpty(precursorUnit))
PrecursorToleranceUnitsBox.Text = precursorUnit;
//mods
currentParam = configFile.FirstOrDefault(x => x.Name == "StaticMods");
if (currentParam != null)
{
var splitString = currentParam.Value.Trim('"').Split();
for (var x = 0; x + 1 < splitString.Length; x += 2)
{
double mass;
if (!double.TryParse(splitString[x + 1], NumberStyles.Number, CultureInfo.InvariantCulture, out mass))
continue;
ModBox.Rows.Add(new object[] { splitString[x], mass, "Static" });
}
}
currentParam = configFile.FirstOrDefault(x => x.Name == "DynamicMods");
if (currentParam != null)
{
var splitString = currentParam.Value.Trim('"').Split();
for (var x = 0; x + 2 < splitString.Length; x += 3)
{
double mass;
if (!double.TryParse(splitString[x + 2], NumberStyles.Number, CultureInfo.InvariantCulture, out mass))
continue;
ModBox.Rows.Add(new object[] { splitString[x], mass, "Dynamic" });
}
}
}
else if (recievedHi.JobType == JobType.Comet)
{
var currentParam = configFile.FirstOrDefault(x => x.Name.ToLower() == "config");
if (currentParam == null)
return;
var cometConfig = CometHandler.FileContentsToCometParams(currentParam.Value);
CometSuffixBox.Text = cometConfig.OutputSuffix;
CleavageAgentBox.Text = CometParams.CleavageAgentOptions.First(x=>x.Value == cometConfig.CleavageAgent).Key;
SpecificityBox.SelectedIndex = cometConfig.Specificity;
//tolerance
if (cometConfig.FragmentBinTolerance > 0.5)
FragmentLowRadio.Checked = true;
else
FragmentHighRadio.Checked = true;
if (cometConfig.PrecursorUnit == CometParams.PrecursorUnitOptions.Daltons)
{
PrecursorLowRadio.Checked = true;
PrecursorToleranceUnitsBox.Text = "mz";
}
else
{
PrecursorHighRadio.Checked = true;
PrecursorToleranceUnitsBox.Text = "ppm";
}
PrecursorToleranceBox.Text = cometConfig.PrecursorTolerance.ToString();
//mods
if (cometConfig.StaticCysteineMod > 0)
ModBox.Rows.Add(new object[] {"C", cometConfig.StaticCysteineMod, "Static"});
foreach (var mod in cometConfig.DynamicModifications)
{
if (mod.Residue == "X")
continue;
var residue = (mod.isNterminal() ? "(" : string.Empty) +
mod.Residue.Replace("*", string.Empty) +
(mod.isCterminal() ? ")" : string.Empty);
ModBox.Rows.Add(new object[] {residue, mod.MassChange, "Dynamic"});
}
}
else if (recievedHi.JobType == JobType.MSGF)
{
var currentParam = configFile.FirstOrDefault(x => x.Name.ToLower() == "config");
if (currentParam == null)
return;
var msgfConfig = MSGFHandler.OverloadToMSGFParams(currentParam.Value);
currentParam = configFile.FirstOrDefault(x => x.Name.ToLower() == "mods");
if (currentParam == null)
return;
var msgfMods = MSGFHandler.ModStringToModList(currentParam.Value);
CometSuffixBox.Text = msgfConfig.OutputSuffix;
CleavageAgentBox.Text = MSGFParams.CleavageAgentOptions.First(x => x.Value == msgfConfig.CleavageAgent).Key;
SpecificityBox.SelectedIndex = msgfConfig.Specificity;
////tolerance
//if (msgfConfig.FragmentationMethod == MSGFParams.FragmentationMethodOptions.CID)
// FragmentLowRadio.Checked = true;
//else
// FragmentHighRadio.Checked = true;
if (msgfConfig.PrecursorToleranceUnits == MSGFParams.PrecursorToleranceUnitOptions.Daltons)
{
PrecursorLowRadio.Checked = true;
PrecursorToleranceUnitsBox.Text = "mz";
}
else
{
PrecursorHighRadio.Checked = true;
PrecursorToleranceUnitsBox.Text = "ppm";
}
PrecursorToleranceBox.Text = msgfConfig.PrecursorTolerance.ToString();
//mods
foreach (var mod in msgfMods)
ModBox.Rows.Add(new object[] {mod.Residue, mod.Mass, mod.Type});
}
}
private void ConfigWizard_Load(object sender, EventArgs e)
{
//set up panel reference
_panelReference = new Dictionary<int, Panel>();
var index = 1;
var indexSet = new HashSet<int>();
foreach (Panel panel in splitContainer1.Panel1.Controls.Cast<Panel>().ToList().OrderBy(x=>x.TabIndex))
{
//Note, panel order is determined by TabIndex
if (!indexSet.Add(panel.TabIndex))
throw new Exception("Duplicate panel index found. "+
"If this error is encountered outside development please contact "+
"the person in charge of BumberDash upkeep.");
_panelReference.Add(index, panel);
index++;
}
_finalPanel = _panelReference.Count;
//set default values
ModTypeBox.Text = "Dynamic";
PrecursorToleranceUnitsBox.Text = "ppm";
FragmentToleranceUnitsBox.Text = "ppm";
SpecificityBox.Text = "Fully-Specific";
ModBox.Rows.Add(new object[] {"C", 57.021464.ToString(), "Static"});
ModBox.Rows.Add(new object[] { "M", 15.994915.ToString(), "Dynamic" });
DBSavedBrowse.Enabled = (!string.IsNullOrEmpty(Properties.Settings.Default.DatabaseFolder)
&& Directory.Exists(Properties.Settings.Default.DatabaseFolder));
LibSavedBrowse.Enabled = (!string.IsNullOrEmpty(Properties.Settings.Default.LibraryFolder)
&& Directory.Exists(Properties.Settings.Default.LibraryFolder));
//set up unimod suggestions
var uniModSuggestions = new List<string>();
foreach (var item in Util.UnimodLookup.FullUnimodList)
uniModSuggestions.Add(item.MonoMass + " " + item.Name);
var source = new AutoCompleteStringCollection();
source.AddRange(uniModSuggestions.ToArray());
ModMassBox.AutoCompleteMode = AutoCompleteMode.Suggest;
ModMassBox.AutoCompleteSource = AutoCompleteSource.CustomSource;
ModMassBox.AutoCompleteCustomSource = source;
ModMassBox.TextChanged += (x, y) =>
{
if (ModMassBox.Text.Contains(" "))
ModMassBox.Text = ModMassBox.Text.Remove(ModMassBox.Text.IndexOf(' '));
};
foreach (var kvp in _panelReference)
{
if (kvp.Key == _currentPanel)
{
kvp.Value.Dock = DockStyle.Fill;
kvp.Value.Visible = true;
continue;
}
kvp.Value.Visible = false;
kvp.Value.Dock = DockStyle.None;
}
if (_currentJob == null)
_currentJob = new HistoryItem();
else
SetHistoryItem(_currentJob);
}
public ConfigWizard(IList<ConfigFile> templateList)
{
InitializeComponent();
_currentJob = null;
_templateList = templateList;
}
/// <summary>
/// Starts Bumbershoot utility based on current row and destination program
/// </summary>
private void ProcessJob(HistoryItem hi)
{
var argumentString = new StringBuilder();
string configString;
_killed = false;
ProcessStartInfo psi;
if (hi.Cpus > 0)
argumentString.Append(string.Format("-cpus {0} ", hi.Cpus));
var workingDirectory = hi.OutputDirectory.TrimEnd('*');
switch (_destinationProgram)
{
case "MyriMatch":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\MyriMatch\myrimatch.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
configString = hi.InitialConfigFile.FilePath == "--Custom--"
? PropertyListToOverrideString(hi.InitialConfigFile.PropertyList)
: string.Format("-cfg \"{0}\" ", hi.InitialConfigFile.FilePath);
//continue to set up argument string
argumentString.Append(String.Format("{0}-ProteinDatabase \"{1}\"",
configString,
hi.ProteinDatabase));
//add files to scan to argument string
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
}
else
foreach (var file in hi.FileList)
{
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
break;
case "DirecTag":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\DirecTag\directag.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
configString = hi.InitialConfigFile.FilePath == "--Custom--"
? PropertyListToOverrideString(hi.InitialConfigFile.PropertyList)
: string.Format("-cfg \"{0}\" ", hi.InitialConfigFile.FilePath);
//HACK: Remove when deisotoping is usable
configString += string.Format("-{0} {1} ", "DeisotopingMode", "0");
//continue to set up argument string
argumentString.Append(configString.Trim());
//add files to scan to argument string
_direcTagMask = null;
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
_direcTagMask = fullMask;
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
}
else
foreach (var file in hi.FileList)
{
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
break;
case "TagRecon":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\TagRecon\tagrecon.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
if (hi.TagConfigFile.FilePath == "--Custom--")
{
configString = PropertyListToOverrideString(hi.TagConfigFile.PropertyList);
//use intranal blosum and unimod files if not specified
if (!configString.Contains("-Blosum "))
configString += string.Format("-{0} \"{1}\" ", "Blosum",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\blosum62.fas"));
if (!configString.Contains("UnimodXML"))
configString += string.Format("-{0} \"{1}\" ", "UnimodXML",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\unimod.xml"));
}
else
{
configString = string.Format("-cfg \"{0}\" ", hi.TagConfigFile.FilePath);
var configCheck = new StreamReader(hi.TagConfigFile.FilePath);
var entireFile = configCheck.ReadToEnd();
configCheck.Close();
if (!entireFile.Contains("Blosum ="))
configString += string.Format("-{0} \"{1}\" ", "Blosum",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\blosum62.fas"));
if (!entireFile.Contains("UnimodXML ="))
configString += string.Format("-{0} \"{1}\" ", "UnimodXML",
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory,
@"lib\Bumbershoot\TagRecon\unimod.xml"));
}
//continue to set up argument string
argumentString.Append(String.Format("{0}-ProteinDatabase \"{1}\"",
configString,
hi.ProteinDatabase));
//add files to scan to argument string
foreach (var file in _completedFiles)
{
argumentString.AppendFormat(" \"{0}\"", Path.Combine(hi.OutputDirectory.TrimEnd('*'), file));
_filesToProcess++;
}
break;
case "Pepitome":
//Set location of the program
psi = new ProcessStartInfo(String.Format(@"""{0}\lib\Bumbershoot\Pepitome\pepitome.exe""",
AppDomain.CurrentDomain.BaseDirectory));
//determine configuration
configString = hi.InitialConfigFile.FilePath == "--Custom--"
? PropertyListToOverrideString(hi.InitialConfigFile.PropertyList)
: string.Format("-cfg \"{0}\" ", hi.InitialConfigFile.FilePath);
//continue to set up argument string
argumentString.Append(String.Format("{0}-ProteinDatabase \"{1}\" -SpectralLibrary \"{2}\"",
configString, hi.ProteinDatabase, hi.SpectralLibrary));
//add files to scan to argument string
if (hi.FileList.Count == 1 && hi.FileList[0].FilePath.StartsWith("!"))
{
var fullMask = hi.FileList[0].FilePath.Trim('!');
var initialDir = Path.GetDirectoryName(fullMask);
var mask = Path.GetFileName(fullMask);
var maskedFiles = Directory.GetFiles(initialDir, mask);
argumentString.Append(String.Format(" \"{0}\"", fullMask));
_filesToProcess = maskedFiles.Length;
}
else
foreach (var file in hi.FileList)
{
argumentString.Append(String.Format(" {0}", file.FilePath));
_filesToProcess++;
}
break;
default:
//should never be called, throw error if it is
throw new Exception(String.Format("Destination Program not set to known value: {0}",
_destinationProgram));
}
psi.WorkingDirectory = workingDirectory;
psi.Arguments = argumentString.ToString();
var commandGiven = (string.Format("Command given:{0}{1}>{2} {3}{0}{0}", Environment.NewLine, psi.WorkingDirectory, psi.FileName, psi.Arguments));
SendToLog(commandGiven);
//Make sure window stays hidden
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
psi.UseShellExecute = false;
psi.CreateNoWindow = true;
_runningProgram = new Process
{
StartInfo = psi,
EnableRaisingEvents = true
};
_runningProgram.Start();
_runningProgram.PriorityClass = ProcessPriorityClass.BelowNormal;
_runningProgram.BeginOutputReadLine();
_runningProgram.OutputDataReceived += DataReceived;
_runningProgram.BeginErrorReadLine();
_runningProgram.ErrorDataReceived += ErrorCaught;
_runningProgram.Exited += (x, y) =>
{
var bgWait = new BackgroundWorker();
bgWait.DoWork += (zzz, e) =>
{
SendToLog(" ---Program exit detected---");
Thread.Sleep(100);
SendToLog(" ---Calculating results---");
var a = ((object[])e.Argument)[0];
var b = (EventArgs)((object[])e.Argument)[1];
ProgramExited(a, b);
};
bgWait.RunWorkerAsync(new object[] { x, y });
//ProgramExited(x,y);
};
}
private void RunFile(string neededFile, string neededDB, string neededLibrary, string destinationProgram)
{
log= new StringBuilder();
var errorFound = false;
var waitHandle = new AutoResetEvent(false);
var target = new ProgramHandler();
var hi = new HistoryItem
{
JobName = Path.GetDirectoryName(neededFile),
JobType = destinationProgram,
OutputDirectory = _outputDirectory,
ProteinDatabase = neededDB,
SpectralLibrary = destinationProgram == JobType.Library
? neededLibrary
: null,
Cpus = 0,
CurrentStatus = string.Empty,
StartTime = null,
EndTime = null,
RowNumber = 0,
InitialConfigFile = new ConfigFile()
{
FilePath = "--Custom--",
PropertyList = new List<ConfigProperty>()
},
TagConfigFile = destinationProgram == JobType.Tag
? new ConfigFile()
{
FilePath = "--Custom--",
PropertyList = new List<ConfigProperty>()
}
: null
};
//File List
hi.FileList = new List<InputFile>
{
new InputFile
{
FilePath = "\"" + neededFile + "\"",
HistoryItem = hi
}
};
//set end event
target.JobFinished = (x, y) =>
{
errorFound = y;
if (!errorFound && x)
target.StartNewJob(0, hi);
else
waitHandle.Set(); // signal that the finished event was raised
};
target.LogUpdate = x => log.AppendLine(x);
target.ErrorForward = x => log.AppendLine(x);
// call the async method
target.StartNewJob(0, hi);
// Wait until the event handler is invoked);
if (!waitHandle.WaitOne(60000, false))
{
var logstring1 = log.ToString();
if (logstring1 != "Test Case")
Assert.Fail("Test timed out." + Environment.NewLine + logstring1);
}
var logstring = log.ToString();
Assert.IsFalse(errorFound, "Not as many output files as input" + Environment.NewLine + logstring);
}
/// <summary>
/// Show AddJobForm with given properties already filled out
/// </summary>
/// <param name="oldHi"></param>
private void ShowCloneBox(HistoryItem oldHi)
{
var templateList = _session.QueryOver<ConfigFile>().Where(x => x.FilePath == "Template").List();
var addJob = new ConfigWizard(oldHi, templateList, false);
if (addJob.ShowDialog() == DialogResult.OK)
{
var items = addJob.GetHistoryItems();
foreach (var hi in items)
InsertRowFromHistoryItem(hi, JobQueueDGV.Rows.Count - 1);
_programmaticallyPaused = false;
}
CheckForRunableJob();
}
/// <summary>
/// Adds job based on given HistoryItem
/// </summary>
/// <param name="hi"></param>
/// <param name="row"></param>
private void InsertRowFromHistoryItem(HistoryItem hi, int row)
{
//Fill in job type if needed
if (hi.JobType == null)
{
hi.JobType = hi.TagConfigFile == null ? JobType.Myrimatch : JobType.Tag;
lock (_session)
{
_session.Save(hi);
_session.Flush();
}
}
#region Check for duplicate config files
//Check initial config file
var oldConfigList = _session.QueryOver<ConfigFile>().
Where(x => x.FilePath == hi.InitialConfigFile.FilePath && x.DestinationProgram == hi.InitialConfigFile.DestinationProgram).OrderBy(y => y.FirstUsedDate).Asc.List();
//Hack: initialize used by list to keep it from being deleted
//on program close (if job has not finished)
hi.InitialConfigFile.UsedByList = new List<HistoryItem> { hi };
hi.InitialConfigFile.FirstUsedDate = DateTime.Now;
foreach (var item in oldConfigList)
{
var foundDuplicate = true;
if (item.PropertyList.Count == hi.InitialConfigFile.PropertyList.Count)
{
for (var oldProperty = 0; oldProperty < item.PropertyList.Count; oldProperty++)
{
var property = item.PropertyList[oldProperty];
var otherPropertyList = hi.InitialConfigFile.PropertyList.Where(
x => (x.Name == property.Name &&
x.Value == property.Value)).ToList();
var otherProperty = otherPropertyList.Any() ? otherPropertyList[0] : null;
if (otherProperty == null)
{
foundDuplicate = false;
break;
}
}
}
else
foundDuplicate = false;
if (foundDuplicate)
{
hi.InitialConfigFile = item;
break;
}
}
//Check tag config file
if (hi.TagConfigFile != null)
{
oldConfigList = _session.QueryOver<ConfigFile>().
Where(x => x.FilePath == hi.TagConfigFile.FilePath && x.DestinationProgram == hi.TagConfigFile.DestinationProgram).OrderBy(y => y.FirstUsedDate).Asc.List();
//Hack: initialize used by list to keep it from being deleted
//on program close (if job has not finished)
hi.TagConfigFile.UsedByList = new List<HistoryItem> { hi };
hi.TagConfigFile.FirstUsedDate = DateTime.Now;
foreach (var item in oldConfigList)
{
var foundDuplicate = true;
if (item.PropertyList.Count == hi.TagConfigFile.PropertyList.Count)
{
for (var oldProperty = 0; oldProperty < item.PropertyList.Count; oldProperty++)
{
var property = item.PropertyList[oldProperty];
var otherPropertyList = hi.InitialConfigFile.PropertyList.Where(
x => (x.Name == property.Name &&
x.Value == property.Value)).ToList();
var otherProperty = otherPropertyList.Any() ? otherPropertyList[0] : null;
if (otherProperty == null)
{
foundDuplicate = false;
break;
}
}
}
else
foundDuplicate = false;
if (foundDuplicate)
{
hi.TagConfigFile = item;
break;
}
}
}
#endregion
var values = new object[6];
//fill values list with appropriate info
values[0] = hi.JobName;
values[1] = (new DirectoryInfo(hi.OutputDirectory.TrimEnd('+').TrimEnd('*'))).Name;
if (hi.JobType == JobType.Library)
values[2] = string.Format("{0} / {1}", Path.GetFileName(hi.ProteinDatabase),
Path.GetFileName(hi.SpectralLibrary));
else
values[2] = Path.GetFileName(hi.ProteinDatabase);
if (hi.TagConfigFile != null)
{
values[3] = String.Format("{0} / {1}", hi.InitialConfigFile.Name ?? Path.GetFileNameWithoutExtension(hi.InitialConfigFile.FilePath),
hi.TagConfigFile.Name ?? Path.GetFileNameWithoutExtension(hi.TagConfigFile.FilePath));
values[4] = JobType.Tag;
}
else
{
values[3] = hi.InitialConfigFile.Name ?? Path.GetFileNameWithoutExtension(hi.InitialConfigFile.FilePath);
values[4] = hi.JobType;
}
if (hi.CurrentStatus == "Finished")
values[5] = 100;
else
values[5] = 0;
//Add row and set current status
JobQueueDGV.Rows.Insert(row, values);
JobQueueDGV.Rows[row].Tag = hi.CurrentStatus;
//Adjust row appearance if status is special
if (hi.CurrentStatus == "Locked")
for (int x = 0; x < 6; x++)
JobQueueDGV.Rows[row].Cells[x].Style.BackColor = Color.Wheat;
else if (hi.CurrentStatus == "Unsuccessful")
JobQueueDGV[5, row].Style.BackColor = Color.LightPink;
//Add tooltip to name cell listing file names
var tempString = string.Empty;
foreach (var i in hi.FileList)
tempString += i.FilePath + Environment.NewLine;
tempString = tempString.Trim();
JobQueueDGV.Rows[row].Cells[0].ToolTipText = tempString;
//Hold on to history item for future use
JobQueueDGV.Rows[row].Cells[0].Tag = hi;
//Add full output directory to tooltip
JobQueueDGV.Rows[row].Cells[1].ToolTipText = hi.OutputDirectory;
//Myrimatch File Name
JobQueueDGV.Rows[row].Cells[2].ToolTipText = hi.ProteinDatabase +
(hi.SpectralLibrary == null
? string.Empty
: Environment.NewLine + hi.SpectralLibrary);
//Configs
bool databaseCustom = hi.InitialConfigFile.FilePath == "--Custom--";
if (hi.TagConfigFile != null)
{
bool tagCustom = hi.TagConfigFile.FilePath == "--Custom--";
JobQueueDGV.Rows[row].Cells[3].ToolTipText =
string.Format("{0}{1}{2}{1}{3}",
databaseCustom ? CreatePropertyStringFromConfig(hi.InitialConfigFile)
: hi.InitialConfigFile.FilePath, Environment.NewLine, new string('-', 20),
tagCustom ? CreatePropertyStringFromConfig(hi.TagConfigFile)
: hi.TagConfigFile.FilePath);
}
else
JobQueueDGV.Rows[row].Cells[3].ToolTipText = databaseCustom
? CreatePropertyStringFromConfig(hi.InitialConfigFile)
: hi.InitialConfigFile.FilePath;
//last button
JobQueueDGV.Rows[row].Cells[6].Value = "X";
hi.RowNumber = row;
_session.SaveOrUpdate(hi.InitialConfigFile);
if (hi.TagConfigFile != null)
_session.SaveOrUpdate(hi.TagConfigFile);
_session.SaveOrUpdate(hi);
_session.Flush();
}
