/// <summary>
/// Shows a dialog prompting user to decide whether to use embedded spectra when external spectra are preferred but cannot be found.
/// Returns 'normal' if the user wants Embedded spectra, 'option1' to retry finding the external spectra, or to 'cancel' to abort the library build.
/// </summary>
public static UpdateProgressResponse ShowLibraryMissingExternalSpectraError(Control parentWindow, Exception errorException)
{
// E.g. could not find external raw data for MaxQuant msms.txt; ask user if they want to retry with "prefer embedded spectra" option
if (!BiblioSpecLiteBuilder.IsLibraryMissingExternalSpectraError(errorException, out string spectrumFilename, out string resultsFilepath))
{
throw new InvalidOperationException(@"IsLibraryMissingExternalSpectraError returned false");
}
// TODO: parse supported file extensions from BiblioSpec or ProteoWizard
var dialogResult = MultiButtonMsgDlg.Show(parentWindow,
string.Format(Resources.VendorIssueHelper_ShowLibraryMissingExternalSpectraError_Could_not_find_an_external_spectrum_file_matching__0__in_the_same_directory_as_the_MaxQuant_input_file__1__,
spectrumFilename, resultsFilepath) +
string.Format(Resources.VendorIssueHelper_ShowLibraryMissingExternalSpectraError_ButtonDescriptionsSupportsExtensions__0__, BiblioSpecLiteBuilder.BiblioSpecSupportedFileExtensions),
Resources.BiblioSpecLiteBuilder_Embedded,
Resources.AlertDlg_GetDefaultButtonText__Retry, true);
switch (dialogResult)
{
case DialogResult.Cancel: return(UpdateProgressResponse.cancel);
case DialogResult.Yes: return(UpdateProgressResponse.normal);
case DialogResult.No: return(UpdateProgressResponse.option1);
default:
throw new ArgumentOutOfRangeException();
}
}
private void BuildLibrary(string inputDir, IEnumerable <string> inputFiles, string libraryPath,
bool keepRedundant, bool includeAmbiguous, bool filterPeptides, bool append, IrtStandard irtStandard)
{
EnsurePeptideSettings();
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(PeptideSettingsUI.ShowBuildLibraryDlg);
List <string> inputPaths = null;
if (inputFiles != null)
{
inputPaths = new List <string>(inputFiles).ConvertAll(f => Path.Combine(inputDir, f));
}
string autoLibPath = null;
RunUI(() =>
{
if (libraryPath != null)
{
buildLibraryDlg.LibraryPath = libraryPath;
}
buildLibraryDlg.LibraryName = _libraryName;
autoLibPath = buildLibraryDlg.LibraryPath;
buildLibraryDlg.LibraryKeepRedundant = keepRedundant;
buildLibraryDlg.IncludeAmbiguousMatches = includeAmbiguous;
buildLibraryDlg.LibraryFilterPeptides = filterPeptides;
buildLibraryDlg.LibraryBuildAction = (append ?
LibraryBuildAction.Append : LibraryBuildAction.Create);
if (irtStandard != null && !irtStandard.Equals(IrtStandard.EMPTY))
{
buildLibraryDlg.IrtStandard = irtStandard;
}
buildLibraryDlg.OkWizardPage();
if (inputPaths != null)
{
buildLibraryDlg.AddInputFiles(inputPaths);
}
else
{
buildLibraryDlg.AddDirectory(inputDir);
}
});
OkDialog(buildLibraryDlg, buildLibraryDlg.OkWizardPage);
if (inputPaths != null)
{
foreach (var inputFile in inputPaths)
{
if (BiblioSpecLiteBuilder.HasEmbeddedSpectra(inputFile))
{
var embeddedSpectraDlg = WaitForOpenForm <MultiButtonMsgDlg>();
OkDialog(embeddedSpectraDlg, embeddedSpectraDlg.BtnYesClick);
}
}
}
Assert.AreEqual(TestFilesDir.GetTestPath(_libraryName + BiblioSpecLiteSpec.EXT),
autoLibPath);
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <Target> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <Target>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedTarget);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Target,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
if (prositDataSourceRadioButton.Checked)
{
// TODO: Need to figure out a better way to do this, use PrositPeptidePrecursorPair?
var doc = _documentUiContainer.DocumentUI;
var peptides = doc.Peptides.ToArray();
var precursorCount = doc.PeptideTransitionGroupCount;
var peptidesPerPrecursor = new PeptideDocNode[precursorCount];
var precursors = new TransitionGroupDocNode[precursorCount];
int index = 0;
for (var i = 0; i < peptides.Length; ++i)
{
var groups = peptides[i].TransitionGroups.ToArray();
Array.Copy(Enumerable.Repeat(peptides[i], groups.Length).ToArray(), 0, peptidesPerPrecursor, index,
groups.Length);
Array.Copy(groups, 0, precursors, index, groups.Length);
index += groups.Length;
}
try
{
PrositUIHelpers.CheckPrositSettings(this, _skylineWindow);
// Still construct the library builder, otherwise a user might configure Prosit
// incorrectly, causing the build to silently fail
Builder = new PrositLibraryBuilder(doc, name, outputPath, () => true, IrtStandard,
peptidesPerPrecursor, precursors, NCE);
}
catch (Exception ex)
{
_helper.ShowTextBoxError(this, ex.Message);
return(false);
}
}
else
{
Builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Id = Helpers.MakeId(textName.Text),
IrtStandard = _driverStandards.SelectedItem,
PreferEmbeddedSpectra = PreferEmbeddedSpectra
};
}
}
return(true);
}
private bool BuildPeptideSearchLibrary(CancelEventArgs e)
{
// Nothing to build, if now search files were specified
if (!SearchFilenames.Any())
{
var libraries = DocumentContainer.Document.Settings.PeptideSettings.Libraries;
if (!libraries.HasLibraries)
{
return(false);
}
var libSpec = libraries.LibrarySpecs.FirstOrDefault(s => s.IsDocumentLibrary);
return(libSpec != null && LoadPeptideSearchLibrary(libSpec));
}
double cutOffScore;
MessageBoxHelper helper = new MessageBoxHelper(WizardForm);
if (!helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
e.Cancel = true;
return(false);
}
ImportPeptideSearch.CutoffScore = cutOffScore;
BiblioSpecLiteBuilder builder;
try
{
builder = ImportPeptideSearch.GetLibBuilder(DocumentContainer.Document, DocumentContainer.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
builder.PreferEmbeddedSpectra = PreferEmbeddedSpectra;
}
catch (FileEx.DeleteException de)
{
MessageDlg.ShowException(this, de);
return(false);
}
bool retry = false;
do
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_Peptide_Search_Library,
Message = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_document_library_for_peptide_search_,
})
{
// Disable the wizard, because the LongWaitDlg does not
try
{
ImportPeptideSearch.ClosePeptideSearchLibraryStreams(DocumentContainer.Document);
var status = longWaitDlg.PerformWork(WizardForm, 800,
monitor => LibraryManager.BuildLibraryBackground(DocumentContainer, builder, monitor, new LibraryManager.BuildState(null, null)));
if (status.IsError)
{
// E.g. could not find external raw data for MaxQuant msms.txt; ask user if they want to retry with "prefer embedded spectra" option
if (BiblioSpecLiteBuilder.IsLibraryMissingExternalSpectraError(status.ErrorException))
{
var response = ShowLibraryMissingExternalSpectraError(WizardForm, status.ErrorException);
if (response == UpdateProgressResponse.cancel)
{
return(false);
}
else if (response == UpdateProgressResponse.normal)
{
builder.PreferEmbeddedSpectra = true;
}
retry = true;
}
else
{
MessageDlg.ShowException(WizardForm, status.ErrorException);
return(false);
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Failed_to_build_the_library__0__,
Path.GetFileName(BiblioSpecLiteSpec.GetLibraryFileName(DocumentContainer.DocumentFilePath))), x.Message), x);
return(false);
}
}
} while (retry);
var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);
Settings.Default.SpectralLibraryList.Insert(0, docLibSpec);
// Go ahead and load the library - we'll need it for
// the modifications and chromatograms page.
if (!LoadPeptideSearchLibrary(docLibSpec))
{
return(false);
}
var selectedIrtStandard = comboStandards.SelectedItem as IrtStandard;
var addedIrts = false;
if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.EMPTY)
{
addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
}
var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(DocumentContainer.Document, docLibSpec);
if (docNew == null)
{
return(false);
}
if (addedIrts)
{
docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
}
DocumentContainer.ModifyDocumentNoUndo(doc => docNew);
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
{
MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
}
return(true);
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
string authority = null;
string id = null;
if (libraryBuildAction == LibraryBuildAction.Create)
{
authority = LibraryAuthority;
if (Uri.CheckHostName(authority) != UriHostNameType.Dns)
{
_helper.ShowTextBoxError(textAuthority, Resources.BuildLibraryDlg_ValidateBuilder_The_lab_authority_name__0__is_not_valid_This_should_look_like_an_internet_server_address_e_g_mylab_myu_edu_and_be_unlikely_to_be_used_by_any_other_lab_but_need_not_refer_to_an_actual_server,
authority);
return(false);
}
Settings.Default.LibraryAuthority = authority;
id = textID.Text;
if (!Regex.IsMatch(id, @"\w[0-9A-Za-z_\-]*")) // Not L10N: Easier to keep IDs restricted to these values.
{
_helper.ShowTextBoxError(textID, Resources.BuildLibraryDlg_ValidateBuilder_The_library_identifier__0__is_not_valid_Identifiers_start_with_a_letter_number_or_underscore_and_contain_only_letters_numbers_underscores_and_dashes, id);
return(false);
}
}
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <string> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <string>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedSequence);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Sequence,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
_builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Authority = authority,
Id = id
};
}
return(true);
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <Target> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <Target>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedTarget);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Target,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
_builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Id = Helpers.MakeId(textName.Text),
IrtStandard = comboStandards.SelectedItem as IrtStandard
};
}
return(true);
}
