public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, TransitionGroupDocNode nodeTranGroup,
int resultsIndex, int? resultsFile, bool subsequent, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
PeakMatchData referenceTarget;
PeakMatchData[] referenceMatchData;
DateTime? runTime;
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out referenceTarget, out referenceMatchData, out runTime);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
for (int j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (!resultsFile.HasValue || resultsFile.Value == j)) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return doc;
}
private void QueryPeptideProteins(ILongWaitBroker longWaitBroker)
{
List <HashSet <Protein> > peptideProteins = new List <HashSet <Protein> >();
if (BackgroundProteome != null)
{
using (var proteomeDb = BackgroundProteome.OpenProteomeDb())
{
Digestion digestion = BackgroundProteome.GetDigestion(proteomeDb, SrmDocument.Settings.PeptideSettings);
foreach (var peptideDocNode in _peptideDocNodes)
{
HashSet <Protein> proteins = new HashSet <Protein>();
if (digestion != null)
{
if (longWaitBroker.IsCanceled)
{
return;
}
foreach (Protein protein in digestion.GetProteinsWithSequence(peptideDocNode.Peptide.Sequence))
{
if (protein.Sequence == PeptideGroupDocNode.PeptideGroup.Sequence)
{
_targetIsInBackgroundProteome = true;
continue;
}
proteins.Add(protein);
}
}
peptideProteins.Add(proteins);
}
}
}
_peptideProteins = peptideProteins;
}
private IEnumerable <string> DownloadPackages(ILongWaitBroker waitBroker, IEnumerable <string> packagesToDownload)
{
ICollection <string> downloadPaths = new Collection <string>();
ICollection <string> failedDownloads = new Collection <string>();
using (var webClient = TestDownloadClient ?? new MultiFileAsynchronousDownloadClient(waitBroker, PackageUris.Count))
{
foreach (var package in packagesToDownload)
{
Match file = Regex.Match(package, @"[^/]*$");
string downloadPath = Path.GetTempPath() + file;
if (webClient.DownloadFileAsync(new Uri(package), downloadPath))
{
downloadPaths.Add(downloadPath);
}
else
{
failedDownloads.Add(package);
}
}
}
if (failedDownloads.Count != 0)
{
throw new ToolExecutionException(
TextUtil.LineSeparate(
Resources.PythonInstaller_DownloadPackages_Failed_to_download_the_following_packages_,
string.Empty,
TextUtil.LineSeparate(failedDownloads),
string.Empty,
Resources.PythonInstaller_DownloadPython_Check_your_network_connection_or_contact_the_tool_provider_for_installation_support_));
}
return(downloadPaths);
}
private void DownloadR(ILongWaitBroker longWaitBroker)
{
// the repository containing the downloadable R exes
const string baseUri = "http://cran.r-project.org/bin/windows/base/";
// format the file name, e.g. R-2.15.2-win.exe
string exe = @"R-" + _version + @"-win.exe";
// create the download path for the file
DownloadPath = Path.GetTempPath() + exe;
// create the webclient
using (var webClient = TestDownloadClient ?? new MultiFileAsynchronousDownloadClient(longWaitBroker, 2))
{
// First try downloading it as if it is the most recent release of R. The most
// recent version is stored in a different location of the CRAN repo than older versions.
// Otherwise, check and see if it is an older release
var recentUri = new Uri(baseUri + exe);
var olderUri = new Uri(baseUri + @"old/" + _version + @"/" + exe);
if (!webClient.DownloadFileAsync(recentUri, DownloadPath) && !webClient.DownloadFileAsync(olderUri, DownloadPath))
{
throw new ToolExecutionException(
TextUtil.LineSeparate(
Resources.RInstaller_DownloadR_Download_failed_,
Resources
.RInstaller_DownloadPackages_Check_your_network_connection_or_contact_the_tool_provider_for_installation_support_));
}
}
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
if (FailDownload)
{
throw new ToolExecutionException(Resources.TestToolStoreClient_GetToolZipFile_Error_downloading_tool);
}
if (TestDownloadPath != null)
{
return(TestDownloadPath);
}
foreach (var item in ToolStoreItems ?? GetToolStoreItems())
{
if (item.Identifier.Equals(packageIdentifier))
{
string fileName = Path.GetFileName(item.FilePath);
if (fileName == null)
{
throw new ToolExecutionException(Resources.TestToolStoreClient_GetToolZipFile_Error_downloading_tool);
}
string path = Path.Combine(directory, fileName);
File.Copy(item.FilePath, path, true);
return(path);
}
}
throw new ToolExecutionException(Resources.TestToolStoreClient_GetToolZipFile_Cannot_find_a_file_with_that_identifier_);
}
private void FindDataFiles(string directory, bool overwrite, ILongWaitBroker longWaitBroker)
{
// Don't search if every spectrum source file has an exact match and an alternate match
if (directory == null || !Directory.Exists(directory) || (!overwrite && SpectrumSourceFiles.Values.All(s => s.HasMatches)))
{
return;
}
if (longWaitBroker != null)
{
longWaitBroker.Message =
string.Format(Resources.ImportResultsControl_FindResultsFiles_Searching_for_matching_results_files_in__0__, directory);
}
try
{
foreach (string entry in Directory.EnumerateFileSystemEntries(directory))
{
if (longWaitBroker != null && longWaitBroker.IsCanceled)
{
return;
}
if (entry != null && DataSourceUtil.IsDataSource(entry))
{
TryMatch(entry, overwrite);
}
}
}
// ReSharper disable once EmptyGeneralCatchClause
catch (Exception)
{
// No permissions on folder
}
}
/// <summary>
/// Pastes tab delimited data into rows and columns starting from the current cell.
/// If an error is encountered (e.g. type conversion), then a message is displayed,
/// and the focus is left in the cell which had an error.
/// Returns true if any changes were made to the document, false if there were no
/// changes.
/// </summary>
private bool Paste(ILongWaitBroker longWaitBroker, TextReader reader)
{
bool anyChanges = false;
var columnsByDisplayIndex =
DataGridView.Columns.Cast <DataGridViewColumn>().Where(column => column.Visible).ToArray();
Array.Sort(columnsByDisplayIndex, (col1, col2) => col1.DisplayIndex.CompareTo(col2.DisplayIndex));
int iFirstCol;
int iFirstRow;
if (null == DataGridView.CurrentCell)
{
iFirstRow = 0;
iFirstCol = 0;
}
else
{
iFirstCol = columnsByDisplayIndex.IndexOf(col => col.Index == DataGridView.CurrentCell.ColumnIndex);
iFirstRow = DataGridView.CurrentCell.RowIndex;
}
for (int iRow = iFirstRow; iRow < DataGridView.Rows.Count; iRow++)
{
if (longWaitBroker.IsCanceled)
{
return(anyChanges);
}
longWaitBroker.Message = string.Format(Resources.DataGridViewPasteHandler_Paste_Pasting_row__0_, iRow + 1);
string line = reader.ReadLine();
if (null == line)
{
return(anyChanges);
}
var row = DataGridView.Rows[iRow];
using (var values = SplitLine(line).GetEnumerator())
{
for (int iCol = iFirstCol; iCol < columnsByDisplayIndex.Length; iCol++)
{
if (!values.MoveNext())
{
break;
}
var column = columnsByDisplayIndex[iCol];
if (column.ReadOnly)
{
continue;
}
if (!TrySetValue(row.Cells[column.Index], values.Current))
{
return(anyChanges);
}
anyChanges = true;
}
}
}
return(anyChanges);
}
// Extract
public void ExtractTutorial(ILongWaitBroker waitBroker)
{
using (ZipFile zip = ZipFile.Read(getTempPath()))
{
ExpectedSize = zip.Entries.Sum(entry => entry.UncompressedSize);
zip.ExtractProgress += (s, e) => TutorialFile_ExtractProgress(s, e, waitBroker);
var extractDir = getExtractPath();
var skyFileToOpen = Path.Combine(extractDir ?? string.Empty, SkyFileLocationInZip);
foreach (var entry in zip.Entries.ToList())
{
entry.FileName = entry.FileName.Substring(entry.FileName.IndexOf('/')); // Gets rid of everything up to and including first '/'.
if (string.IsNullOrEmpty(entry.FileName))
{
continue;
}
if (waitBroker.IsCanceled)
{
break;
}
try
{
entry.Extract(extractDir);
ExtractedSize += entry.UncompressedSize;
}
catch (Exception)
{
if (!waitBroker.IsCanceled)
{
throw;
}
}
}
Program.MainWindow.BeginInvoke(new Action(() =>
{
if (!string.IsNullOrEmpty(SkyFileLocationInZip) && !string.IsNullOrEmpty(ExtractPath))
{
Program.MainWindow.OpenFile(skyFileToOpen);
}
else
{
Program.MainWindow.NewDocument(true);
}
if (string.IsNullOrEmpty(SkyFileLocationInZip))
{
MessageDlg.Show(Program.MainWindow,
string.Format(Resources.ActionTutorial_client_DownloadFileCompleted_File_saved_at___0_, extractDir));
}
Process.Start(PdfFileLocation); // Opens Tutorial PDF in users default browser.
}));
}
}
// Download
public void DownloadTutorials(ILongWaitBroker waitBroker)
{
WaitBroker = waitBroker;
WaitBroker.ProgressValue = Convert.ToInt32(Progress * 100);
WebClient client = new WebClient
{
CachePolicy = new RequestCachePolicy(RequestCacheLevel.NoCacheNoStore),
};
client.DownloadProgressChanged += client_DownloadProgressChanged;
client.DownloadFile(new Uri(TutorialZipFileLocation), getTempPath());
}
private static void CopyOldTools(string outerToolsFolderPath, ILongWaitBroker broker)
{
//Copy tools to a different folder then Directory.Move if successful.
string tempOuterToolsFolderPath = string.Concat(outerToolsFolderPath, @"_installing");
if (Directory.Exists(tempOuterToolsFolderPath))
{
DirectoryEx.SafeDelete(tempOuterToolsFolderPath);
// Not sure this is necessay, but just to be safe
if (Directory.Exists(tempOuterToolsFolderPath))
{
throw new Exception(Resources.Program_CopyOldTools_Error_copying_external_tools_from_previous_installation);
}
}
// Must create the tools directory to avoid ending up here again next time
Directory.CreateDirectory(tempOuterToolsFolderPath);
ToolList toolList = Settings.Default.ToolList;
int numTools = toolList.Count;
const int endValue = 100;
int progressValue = 0;
// ReSharper disable once UselessBinaryOperation (in case we decide to start at progress>0 for display purposes)
int increment = (endValue - progressValue) / (numTools + 1);
foreach (var tool in toolList)
{
string toolDirPath = tool.ToolDirPath;
if (!string.IsNullOrEmpty(toolDirPath) && Directory.Exists(toolDirPath))
{
string foldername = Path.GetFileName(toolDirPath);
string newDir = Path.Combine(outerToolsFolderPath, foldername);
string tempNewDir = Path.Combine(tempOuterToolsFolderPath, foldername);
if (!Directory.Exists(tempNewDir))
{
DirectoryEx.DirectoryCopy(toolDirPath, tempNewDir, true);
}
tool.ToolDirPath = newDir; // Update the tool to point to its new directory.
tool.ArgsCollectorDllPath = tool.ArgsCollectorDllPath.Replace(toolDirPath, newDir);
}
if (broker.IsCanceled)
{
// Don't leave around a corrupted directory
DirectoryEx.SafeDelete(tempOuterToolsFolderPath);
return;
}
progressValue += increment;
broker.ProgressValue = progressValue;
}
Directory.Move(tempOuterToolsFolderPath, outerToolsFolderPath);
Settings.Default.ToolList = ToolList.CopyTools(toolList);
}
private void update_ProgressChanged(UpdateProgress e, ILongWaitBroker broker)
{
if (broker.IsCanceled)
{
AppDeployment.UpdateAsyncCancel();
}
else
{
long updateBytes = Math.Max(_updateInfo.UpdateSizeBytes ?? 0, e.BytesTotal);
broker.Message = GetProgressMessage(e.BytesCompleted, updateBytes);
broker.ProgressValue = updateBytes == 0
? 0 : (int)Math.Min(99, e.BytesCompleted * 100 / updateBytes);
}
}
private void QueryPeptideProteins(ILongWaitBroker longWaitBroker)
{
List <HashSet <Protein> > peptideProteins = new List <HashSet <Protein> >();
if (BackgroundProteome != null)
{
using (var proteomeDb = BackgroundProteome.OpenProteomeDb(longWaitBroker.CancellationToken))
{
Digestion digestion = proteomeDb.GetDigestion();
if (digestion != null)
{
var peptidesOfInterest = _peptideDocNodes.Select(node => node.Item2.Peptide.Target.Sequence);
var sequenceProteinsDict = digestion.GetProteinsWithSequences(peptidesOfInterest);
if (longWaitBroker.IsCanceled)
{
return;
}
foreach (var tuple in _peptideDocNodes)
{
if (longWaitBroker.IsCanceled)
{
return;
}
var peptideGroup = (PeptideGroup)tuple.Item1.GetIdentity(0);
var peptideDocNode = tuple.Item2;
HashSet <Protein> proteins = new HashSet <Protein>();
var peptideGroupDocNode = PeptideGroupDocNodes.First(g => ReferenceEquals(g.PeptideGroup, peptideGroup));
List <Protein> proteinsForSequence;
if (sequenceProteinsDict.TryGetValue(peptideDocNode.Peptide.Target.Sequence, out proteinsForSequence))
{
if (peptideGroupDocNode != null)
{
foreach (var protein in proteinsForSequence)
{
if (protein.Sequence == peptideGroupDocNode.PeptideGroup.Sequence)
{
_peptidesInBackgroundProteome.Add(tuple.Item1);
continue;
}
proteins.Add(protein);
}
}
}
peptideProteins.Add(proteins);
}
}
}
}
_peptideProteins = peptideProteins;
}
private static void FindInputFiles(string dir, ICollection <string> inputFiles,
ILongWaitBroker broker, double start, double stop)
{
broker.Message = TextUtil.LineSeparate(Resources.BuildLibraryDlg_FindInputFiles_Finding_library_input_files_in,
PathEx.ShortenPathForDisplay(dir));
string[] fileNames = Directory.GetFiles(dir);
Array.Sort(fileNames);
string[] dirs = Directory.GetDirectories(dir);
Array.Sort(dirs);
double startSub = start;
double increment = (stop - start) / (dirs.Length + 1);
const string extPep = BiblioSpecLiteBuilder.EXT_PEP_XML_ONE_DOT;
const string extIdp = BiblioSpecLiteBuilder.EXT_IDP_XML;
bool hasIdp = fileNames.Contains(f => PathEx.HasExtension(f, extIdp));
foreach (string fileName in fileNames)
{
if (IsValidInputFile(fileName))
{
// If the directory has any .idpXML files, then do not add the
// supporting .pepXML files.
if (!hasIdp || !PathEx.HasExtension(fileName, extPep))
{
inputFiles.Add(fileName);
}
}
if (broker.IsCanceled)
{
return;
}
}
startSub += increment;
broker.ProgressValue = (int)startSub;
foreach (string dirSub in dirs)
{
FindInputFiles(dirSub, inputFiles, broker, startSub, startSub + increment);
if (broker.IsCanceled)
{
return;
}
startSub += increment;
broker.ProgressValue = (int)startSub;
}
}
public IEnumerable <FindResult> FindAll(ILongWaitBroker longWaitBroker, SrmDocument document)
{
longWaitBroker.Message = Resources.FindPredicate_FindAll_Found_0_matches;
var customMatches = new HashSet <Bookmark> [FindOptions.CustomFinders.Count];
for (int iFinder = 0; iFinder < FindOptions.CustomFinders.Count; iFinder++)
{
var customFinder = FindOptions.CustomFinders[iFinder];
var bookmarkSet = new HashSet <Bookmark>();
longWaitBroker.Message = string.Format(Resources.FindPredicate_FindAll_Searching_for__0__, customFinder.DisplayName);
foreach (var bookmark in customFinder.FindAll(document))
{
if (longWaitBroker.IsCanceled)
{
yield break;
}
bookmarkSet.Add(bookmark);
}
customMatches[iFinder] = bookmarkSet;
}
var bookmarkEnumerator = new BookmarkEnumerator(document);
int matchCount = 0;
do
{
bookmarkEnumerator.MoveNext();
if (longWaitBroker.IsCanceled)
{
yield break;
}
FindMatch findMatch = null;
for (int iFinder = 0; iFinder < FindOptions.CustomFinders.Count; iFinder++)
{
if (customMatches[iFinder].Contains(bookmarkEnumerator.Current))
{
findMatch = FindOptions.CustomFinders[iFinder].Match(bookmarkEnumerator);
}
}
findMatch = findMatch ?? MatchInternal(bookmarkEnumerator);
if (findMatch != null)
{
matchCount++;
longWaitBroker.Message = matchCount == 1
? Resources.FindPredicate_FindAll_Found_1_match
: string.Format(Resources.FindPredicate_FindAll_Found__0__matches, matchCount);
yield return(new FindResult(this, bookmarkEnumerator, findMatch));
}
} while (!bookmarkEnumerator.AtStart);
}
public IEnumerable<FindResult> FindAll(ILongWaitBroker longWaitBroker, SrmDocument document)
{
longWaitBroker.Message = Resources.FindPredicate_FindAll_Found_0_matches;
var customMatches = new HashSet<Bookmark>[FindOptions.CustomFinders.Count];
for (int iFinder = 0; iFinder < FindOptions.CustomFinders.Count; iFinder++)
{
var customFinder = FindOptions.CustomFinders[iFinder];
var bookmarkSet = new HashSet<Bookmark>();
longWaitBroker.Message = string.Format(Resources.FindPredicate_FindAll_Searching_for__0__, customFinder.DisplayName);
foreach (var bookmark in customFinder.FindAll(document))
{
if (longWaitBroker.IsCanceled)
{
yield break;
}
bookmarkSet.Add(bookmark);
}
customMatches[iFinder] = bookmarkSet;
}
var bookmarkEnumerator = new BookmarkEnumerator(document);
int matchCount = 0;
do
{
bookmarkEnumerator.MoveNext();
if (longWaitBroker.IsCanceled)
{
yield break;
}
FindMatch findMatch = null;
for (int iFinder = 0; iFinder < FindOptions.CustomFinders.Count; iFinder++)
{
if (customMatches[iFinder].Contains(bookmarkEnumerator.Current))
{
findMatch = FindOptions.CustomFinders[iFinder].Match(bookmarkEnumerator);
}
}
findMatch = findMatch ?? MatchInternal(bookmarkEnumerator);
if (findMatch != null)
{
matchCount++;
longWaitBroker.Message = matchCount == 1
? Resources.FindPredicate_FindAll_Found_1_match
: string.Format(Resources.FindPredicate_FindAll_Found__0__matches, matchCount);
yield return new FindResult(this, bookmarkEnumerator, findMatch);
}
} while (!bookmarkEnumerator.AtStart);
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
WebClient webClient = new WebClient();
UriBuilder uri = new UriBuilder(TOOL_STORE_URI)
{
Path = DOWNLOAD_TOOL_URL,
Query = "lsid=" + packageIdentifier // Not L10N
};
byte[] toolZip = webClient.DownloadData(uri.Uri.AbsoluteUri); // Not L10N
string contentDisposition = webClient.ResponseHeaders.Get("Content-Disposition"); // Not L10N
// contentDisposition is filename="ToolBasename.zip"
Match match = Regex.Match(contentDisposition, "^filename=\"(.+)\"$", RegexOptions.IgnoreCase); // Not L10N
string downloadedFile = directory + match.Groups[1].Value;
File.WriteAllBytes(downloadedFile, toolZip);
return(downloadedFile);
}
private void QueryPeptideProteins(ILongWaitBroker longWaitBroker)
{
List <HashSet <Protein> > peptideProteins = new List <HashSet <Protein> >();
if (BackgroundProteome != null)
{
using (var proteomeDb = BackgroundProteome.OpenProteomeDb())
{
Digestion digestion = BackgroundProteome.GetDigestion(proteomeDb, SrmDocument.Settings.PeptideSettings);
if (digestion != null)
{
var peptidesOfInterest = _peptideDocNodes.Select(node => node.Peptide.Sequence);
var sequenceProteinsDict = digestion.GetProteinsWithSequences(peptidesOfInterest, null);
if (longWaitBroker.IsCanceled)
{
return;
}
foreach (var peptideDocNode in _peptideDocNodes)
{
HashSet <Protein> proteins = new HashSet <Protein>();
var peptideGroupDocNode = PeptideGroupDocNodes.First(g => g.Peptides.Contains(peptideDocNode));
List <Protein> proteinsForSequence;
if (sequenceProteinsDict.TryGetValue(peptideDocNode.Peptide.Sequence, out proteinsForSequence))
{
if (peptideGroupDocNode != null)
{
foreach (var protein in proteinsForSequence)
{
if (protein.Sequence == peptideGroupDocNode.PeptideGroup.Sequence)
{
_peptidesInBackgroundProteome.Add(peptideDocNode);
continue;
}
proteins.Add(protein);
}
}
}
peptideProteins.Add(proteins);
}
}
}
}
_peptideProteins = peptideProteins;
}
/// <summary>
/// The asynchronous download client links a webClient to a LongWaitBroker. It supports
/// multiple asynchronous downloads, and updates the associated broker's progress value.
/// </summary>
/// <param name="waitBroker">The associated LongWaitBroker</param>
/// <param name="files">The numbers of file this instance is expected to download. This
/// is used to accurately update the broker's progress value</param>
public MultiFileAsynchronousDownloadClient(ILongWaitBroker waitBroker, int files)
{
_longWaitBroker = waitBroker;
_webClient = new WebClient();
FilesDownloaded = 0;
_webClient.DownloadProgressChanged += (sender, args) =>
{
_longWaitBroker.ProgressValue = (int)Math.Min(100, ((((double)FilesDownloaded) / files) * 100)
+ ((1.0 / files) * args.ProgressPercentage));
};
_webClient.DownloadFileCompleted += (sender, args) =>
{
FilesDownloaded++;
DownloadSucceeded = (args.Error == null);
DownloadComplete = true;
};
}
// Consider: the location of the following python links is assumed to be relatively stable, but could change. We
// might want to package these scripts with Skyline itself to assure that they are available
private void DownloadPip(ILongWaitBroker longWaitBroker)
{
// location of the setuptools install script
const string setupToolsScript = "https://bitbucket.org/pypa/setuptools/downloads/ez_setup.py";
SetupToolsPath = Path.GetTempPath() + @"ez_setup.py";
// location of the pip install script
const string pipScript = "https://raw.github.com/pypa/pip/master/contrib/get-pip.py";
PipPath = Path.GetTempPath() + @"get-pip.py";
using (var webClient = TestPipDownloadClient ?? new MultiFileAsynchronousDownloadClient(longWaitBroker, 2))
{
if (!webClient.DownloadFileAsync(new Uri(setupToolsScript), SetupToolsPath) ||
!webClient.DownloadFileAsync(new Uri(pipScript), PipPath))
{
throw new ToolExecutionException(Resources.PythonInstaller_DownloadPip_Download_failed__Check_your_network_connection_or_contact_Skyline_developers_);
}
}
}
private void DownloadPython(ILongWaitBroker waitBroker)
{
// the base Url for python releases
const string baseUri = "http://python.org/ftp/python/";
// the installer file name, e.g. python-2.7.msi
string fileName = @"python-" + _version + @".msi";
// the fully formed Uri, e.g. http://python.org/ftp/python/2.7/python-2.7.msi
var downloadUri = new Uri(baseUri + _version + @"/" + fileName);
using (var webClient = TestDownloadClient ?? new MultiFileAsynchronousDownloadClient(waitBroker, 1))
{
if (!webClient.DownloadFileAsync(downloadUri, DownloadPath = Path.GetTempPath() + fileName))
{
throw new ToolExecutionException(TextUtil.LineSeparate(
Resources.PythonInstaller_DownloadPython_Download_failed_,
Resources.PythonInstaller_DownloadPython_Check_your_network_connection_or_contact_the_tool_provider_for_installation_support_));
}
}
}
private bool DoFillDown(ILongWaitBroker longWaitBroker, PropertyDescriptor[] propertyDescriptors, int firstRowIndex, int lastRowIndex)
{
bool anyChanges = false;
var firstRowValues = propertyDescriptors.Select(pd => pd.GetValue(BindingListSource[firstRowIndex])).ToArray();
int totalRows = lastRowIndex - firstRowIndex + 1;
for (int iRow = firstRowIndex + 1; iRow <= lastRowIndex; iRow++)
{
if (longWaitBroker.IsCanceled)
{
return(anyChanges);
}
longWaitBroker.ProgressValue = 100 * (iRow - firstRowIndex) / totalRows;
longWaitBroker.Message = string.Format(Resources.DataboundGridControl_DoFillDown_Filling__0___1__rows, iRow - firstRowIndex, totalRows);
var row = BindingListSource[iRow];
for (int icol = 0; icol < propertyDescriptors.Length; icol++)
{
var propertyDescriptor = propertyDescriptors[icol];
try
{
propertyDescriptor.SetValue(row, firstRowValues[icol]);
anyChanges = true;
}
catch (Exception e)
{
MessageDlg.ShowWithException(this, TextUtil.LineSeparate(Resources.DataboundGridControl_DoFillDown_Error_setting_value_,
e.Message), e);
var column = DataGridView.Columns.OfType <DataGridViewColumn>()
.FirstOrDefault(col => col.DataPropertyName == propertyDescriptor.Name);
if (null != column)
{
DataGridView.CurrentCell = DataGridView.Rows[iRow].Cells[column.Index];
}
return(anyChanges);
}
}
}
return(anyChanges);
}
private bool ClearCells(ILongWaitBroker longWaitBroker)
{
if (DataGridView.SelectedRows.Count > 0)
{
return(false);
}
var columnIndexes = DataGridView.SelectedCells.Cast <DataGridViewCell>().Select(cell => cell.ColumnIndex).Distinct().ToArray();
if (columnIndexes.Any(columnIndex => DataGridView.Columns[columnIndex].ReadOnly))
{
return(false);
}
bool anyChanges = false;
var cellsByRow = DataGridView.SelectedCells.Cast <DataGridViewCell>().ToLookup(cell => cell.RowIndex).ToArray();
Array.Sort(cellsByRow, (g1, g2) => g1.Key.CompareTo(g2.Key));
for (int iGrouping = 0; iGrouping < cellsByRow.Length; iGrouping++)
{
if (longWaitBroker.IsCanceled)
{
return(anyChanges);
}
longWaitBroker.ProgressValue = 100 * iGrouping / cellsByRow.Length;
longWaitBroker.Message = string.Format(Resources.DataGridViewPasteHandler_ClearCells_Cleared__0___1__rows, iGrouping, cellsByRow.Length);
var rowGrouping = cellsByRow[iGrouping];
var cells = rowGrouping.ToArray();
Array.Sort(cells, (c1, c2) => c1.ColumnIndex.CompareTo(c2.ColumnIndex));
foreach (var cell in cells)
{
if (!TrySetValue(cell, string.Empty))
{
return(anyChanges);
}
anyChanges = true;
}
}
return(anyChanges);
}
private void DownloadTools(ILongWaitBroker waitBroker,
IEnumerable <ToolUpdateInfo> tools,
out ICollection <ToolUpdateInfo> successfulDownloads,
out ICollection <string> failedDownloads)
{
successfulDownloads = new Collection <ToolUpdateInfo>();
failedDownloads = new Collection <string>();
ToolDir = Directory.CreateDirectory(Path.Combine(Path.GetTempPath(), "ToolDir")); // Not L10N
foreach (var tool in tools)
{
var individualDir = Directory.CreateDirectory(Path.Combine(ToolDir.FullName, tool._packageName));
try
{
tool.FilePath = _updateHelper.GetToolZipFile(waitBroker, tool._packageIdentifer, individualDir.FullName);
successfulDownloads.Add(tool);
}
catch (ToolExecutionException)
{
failedDownloads.Add(tool._packageName);
}
}
}
/// <summary>
/// Matches library peptides to the current document settings and adds them to the document.
/// This needs to be one function so that we can use one LongWaitDlg.
/// </summary>
public void AddAllPeptidesToDocument(ILongWaitBroker broker, AuditLogEntryCreatorList entryCreators)
{
MatchAllPeptides(broker);
if (broker.IsCanceled)
{
return;
}
if (MatchedPeptideCount == 0)
{
return;
}
if (broker.ShowDialog(wnd => EnsureDuplicateProteinFilter(wnd, entryCreators)) == DialogResult.Cancel)
{
return;
}
IdentityPath selectedPath;
IdentityPath toPath = AddAllPeptidesSelectedPath;
DocAllPeptides = AddPeptides(_document, broker, toPath, out selectedPath);
AddAllPeptidesSelectedPath = selectedPath;
}
public void UpdateSpectrumSourceFilesFromDirs(IEnumerable <string> dirPaths, bool overwrite, ILongWaitBroker longWaitBroker)
{
if (!overwrite && SpectrumSourceFiles.Values.All(s => s.HasMatches))
{
return;
}
Array.ForEach(dirPaths.Distinct().ToArray(), dir => FindDataFiles(dir, overwrite, longWaitBroker));
}
private void DownloadPython(ILongWaitBroker waitBroker)
{
// the base Url for python releases
const string baseUri = "http://python.org/ftp/python/"; // Not L10N
// the installer file name, e.g. python-2.7.msi
string fileName = "python-" + _version + ".msi"; // Not L10N
// the fully formed Uri, e.g. http://python.org/ftp/python/2.7/python-2.7.msi
var downloadUri = new Uri(baseUri + _version + "/" + fileName); // Not L10N
using (var webClient = TestDownloadClient ?? new MultiFileAsynchronousDownloadClient(waitBroker, 1))
{
if (!webClient.DownloadFileAsync(downloadUri, DownloadPath = Path.GetTempPath() + fileName))
throw new ToolExecutionException(TextUtil.LineSeparate(
Resources.PythonInstaller_DownloadPython_Download_failed_,
Resources.PythonInstaller_DownloadPython_Check_your_network_connection_or_contact_the_tool_provider_for_installation_support_));
}
}
private static void FindInputFiles(string dir, ICollection<string> inputFiles, ILongWaitBroker broker)
{
broker.ProgressValue = 0;
FindInputFiles(dir, inputFiles, broker, 0, 100);
}
private static void FindInputFiles(string dir, ICollection<string> inputFiles,
ILongWaitBroker broker, double start, double stop)
{
broker.Message = TextUtil.LineSeparate(Resources.BuildLibraryDlg_FindInputFiles_Finding_library_input_files_in,
PathEx.ShortenPathForDisplay(dir));
string[] fileNames = Directory.GetFiles(dir);
Array.Sort(fileNames);
string[] dirs = Directory.GetDirectories(dir);
Array.Sort(dirs);
double startSub = start;
double increment = (stop - start) / (dirs.Length + 1);
const string extPep = BiblioSpecLiteBuilder.EXT_PEP_XML_ONE_DOT;
const string extIdp = BiblioSpecLiteBuilder.EXT_IDP_XML;
bool hasIdp = fileNames.Contains(f => PathEx.HasExtension(f, extIdp));
foreach (string fileName in fileNames)
{
if (IsValidInputFile(fileName))
{
// If the directory has any .idpXML files, then do not add the
// supporting .pepXML files.
if (!hasIdp || !PathEx.HasExtension(fileName, extPep))
inputFiles.Add(fileName);
}
if (broker.IsCanceled)
return;
}
startSub += increment;
broker.ProgressValue = (int) startSub;
foreach (string dirSub in dirs)
{
FindInputFiles(dirSub, inputFiles, broker, startSub, startSub + increment);
if (broker.IsCanceled)
return;
startSub += increment;
broker.ProgressValue = (int)startSub;
}
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
WebClient webClient = new WebClient();
UriBuilder uri = new UriBuilder(TOOL_STORE_URI)
{
Path = DOWNLOAD_TOOL_URL,
Query = "lsid=" + packageIdentifier // Not L10N
};
byte[] toolZip = webClient.DownloadData(uri.Uri.AbsoluteUri); // Not L10N
string contentDisposition = webClient.ResponseHeaders.Get("Content-Disposition"); // Not L10N
// contentDisposition is filename="ToolBasename.zip"
Match match = Regex.Match(contentDisposition, "^filename=\"(.+)\"$", RegexOptions.IgnoreCase); // Not L10N
string downloadedFile = directory + match.Groups[1].Value;
File.WriteAllBytes(downloadedFile, toolZip);
return downloadedFile;
}
private SrmDocument ImportFiles(SrmDocument docOrig,
ILongWaitBroker longWaitBroker,
IList<string> filePaths,
MeasuredResults.MergeAction resultsAction,
bool mergePeptides,
IdentityPath to,
out IdentityPath firstAdded)
{
firstAdded = null;
var docResult = docOrig;
int filesRead = 0;
// Add files in reverse order, so their nodes will end up in the right order.
IdentityPath first = null;
foreach (var filePath in filePaths)
{
if (longWaitBroker != null)
{
if (longWaitBroker.IsCanceled || longWaitBroker.IsDocumentChanged(docOrig))
return docOrig;
longWaitBroker.ProgressValue = filesRead*100/filePaths.Count;
longWaitBroker.Message = string.Format(Resources.SkylineWindow_ImportFiles_Importing__0__, Path.GetFileName(filePath));
}
using (var reader = new StreamReader(filePath))
{
IdentityPath firstAddedForFile, nextAdd;
docResult = docResult.ImportDocumentXml(reader,
filePath,
resultsAction,
mergePeptides,
FindSpectralLibrary,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
to,
out firstAddedForFile,
out nextAdd,
false);
// Add the next document at the specified location
to = nextAdd;
// Store the first added node only for the first document
if (first == null)
first = firstAddedForFile;
}
filesRead++;
}
firstAdded = first;
return docResult;
}
// Download
public void DownloadTutorials(ILongWaitBroker waitBroker)
{
WaitBroker = waitBroker;
WaitBroker.ProgressValue = Convert.ToInt32(Progress * 100);
WebClient client = new WebClient
{
CachePolicy = new RequestCachePolicy(RequestCacheLevel.NoCacheNoStore),
};
client.DownloadProgressChanged += client_DownloadProgressChanged;
client.DownloadFile(new Uri(TutorialZipFileLocation), getTempPath());
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
return _client.GetToolZipFile(waitBroker, packageIdentifier, directory);
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
var client = ToolStoreUtil.CreateClient();
return(client.GetToolZipFile(waitBroker, packageIdentifier, directory));
}
public void PerformWork(ILongWaitBroker broker)
{
_performWork();
}
private void TutorialFile_ExtractProgress(object sender, ExtractProgressEventArgs e, ILongWaitBroker waitBroker)
{
if (waitBroker != null)
{
if (waitBroker.IsCanceled)
{
e.Cancel = true;
return;
}
int progressValue = (int)Math.Round((ExtractedSize + e.BytesTransferred) * 100.0 / ExpectedSize);
if (progressValue != WaitBroker.ProgressValue)
{
waitBroker.ProgressValue = progressValue;
waitBroker.Message = (string.Format(Resources.SrmDocumentSharing_SrmDocumentSharing_ExtractProgress_Extracting__0__,
e.CurrentEntry.FileName));
}
}
}
// Extract
public void ExtractTutorial(ILongWaitBroker waitBroker)
{
using (ZipFile zip = ZipFile.Read(getTempPath()))
{
ExpectedSize = zip.Entries.Sum(entry => entry.UncompressedSize);
zip.ExtractProgress += (s,e) => TutorialFile_ExtractProgress(s,e, waitBroker);
var extractDir = getExtractPath();
var skyFileToOpen = Path.Combine(extractDir ?? string.Empty, SkyFileLocationInZip);
foreach (var entry in zip.Entries.ToList())
{
entry.FileName = entry.FileName.Substring(entry.FileName.IndexOf('/')); // Gets rid of everything up to and including first '/'.
if (string.IsNullOrEmpty(entry.FileName))
{
continue;
}
if (waitBroker.IsCanceled)
break;
try
{
entry.Extract(extractDir);
ExtractedSize += entry.UncompressedSize;
}
catch (Exception)
{
if (!waitBroker.IsCanceled)
throw;
}
}
Program.MainWindow.BeginInvoke(new Action(() =>
{
if (!string.IsNullOrEmpty(SkyFileLocationInZip) && !string.IsNullOrEmpty(ExtractPath))
{
Program.MainWindow.OpenFile(skyFileToOpen);
}
else
{
Program.MainWindow.NewDocument(true);
}
if (string.IsNullOrEmpty(SkyFileLocationInZip))
{
MessageDlg.Show(Program.MainWindow,
string.Format(Resources.ActionTutorial_client_DownloadFileCompleted_File_saved_at___0_, extractDir));
}
Process.Start(PdfFileLocation); // Opens Tutorial PDF in users default browser.
}));
}
}
public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, ref TransitionGroupDocNode nodeTranGroup,
int resultsIndex, ChromFileInfoId resultsFile, bool subsequent, ReplicateValue groupBy, object groupByValue, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out var referenceTarget, out var referenceMatchData, out var runTime);
var annotationCalculator = new AnnotationCalculator(doc);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (var i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
if (groupBy != null)
{
if (!Equals(groupByValue, groupBy.GetValue(annotationCalculator, chromSet)))
{
continue;
}
}
for (var j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (resultsFile == null || ReferenceEquals(resultsFile, fileInfo.FileId))) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
{
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return(doc);
}
/// <summary>
/// Adds all peptides which can be matched to a background proteome to the
/// proteins in the background proteins, and returns a new document with those
/// proteins and peptides added.
/// </summary>
/// <param name="document">The starting document</param>
/// <param name="dictCopy">A dictionary of peptides to peptide matches. All added
/// peptides are removed</param>
/// <param name="broker">For reporting long wait status</param>
/// <param name="toPath">Path to the location in the document to add new items</param>
/// <param name="selectedPath">Path to item in the document that should be selected
/// after this operation is complete</param>
/// <returns>A new document with matching peptides and their proteins addded</returns>
private SrmDocument AddProteomePeptides(SrmDocument document,
Dictionary<PeptideSequenceModKey, PeptideMatch> dictCopy,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Build a list of new PeptideGroupDocNodes to add to the document.
var dictPeptideGroupsNew = new Dictionary<string, PeptideGroupDocNode>();
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = dictCopy.Count;
// Just to make sure this is set
selectedPath = toPath;
foreach (PeptideMatch pepMatch in dictCopy.Values)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = toPath;
return document;
}
// All peptides with protein get processed in this loop. Peptides
// without proteins get added later.
if (pepMatch.Proteins != null)
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
// Peptide should be added to the document,
// unless the NoDuplicates radio was selected and the peptide has more than 1 protein associated with it.
if (pepMatch.Proteins == null ||
(FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.NoDuplicates && pepMatch.Proteins.Count > 1))
continue;
foreach (ProteinInfo protein in pepMatch.Proteins)
{
// Look for the protein in the document.
string name = protein.ProteinMetadata.Name;
var peptideGroupDocNode = FindPeptideGroupDocNode(document, name);
bool foundInDoc = peptideGroupDocNode != null;
bool foundInList = false;
if (!foundInDoc)
{
// If the protein is not already in the document,
// check to see if we have already created a PeptideGroupDocNode for it.
if (dictPeptideGroupsNew.TryGetValue(name, out peptideGroupDocNode))
foundInList = true;
// If not, create a new PeptideGroupDocNode.
else
{
List<ProteinMetadata> alternativeProteins = new List<ProteinMetadata>(protein.Alternatives);
peptideGroupDocNode = new PeptideGroupDocNode(
new FastaSequence(name, protein.ProteinMetadata.Description, alternativeProteins, protein.Sequence),
null, null, new PeptideDocNode[0]);
}
}
// Create a new peptide that matches this protein.
var fastaSequence = peptideGroupDocNode.PeptideGroup as FastaSequence;
var peptideSequence = pepMatch.NodePep.Peptide.Sequence;
// ReSharper disable PossibleNullReferenceException
var begin = fastaSequence.Sequence.IndexOf(peptideSequence, StringComparison.Ordinal);
// ReSharper restore PossibleNullReferenceException
// Create a new PeptideDocNode using this peptide.
var newPeptide = new Peptide(fastaSequence, peptideSequence, begin, begin + peptideSequence.Length,
Settings.PeptideSettings.Enzyme.CountCleavagePoints(peptideSequence));
// Make sure we keep the same children.
PeptideMatch match = pepMatch;
var newNodePep = ((PeptideDocNode) new PeptideDocNode(newPeptide, pepMatch.NodePep.ExplicitMods, pepMatch.NodePep.ExplicitRetentionTime)
.ChangeChildren(pepMatch.NodePep.Children.ToList().ConvertAll(nodeGroup =>
{
// Create copies of the children in order to prevent transition groups with the same
// global indices.
var nodeTranGroup = (TransitionGroupDocNode) nodeGroup;
if(match.Proteins != null && match.Proteins.Count() > 1)
{
nodeTranGroup = (TransitionGroupDocNode) nodeTranGroup.CopyId();
nodeTranGroup = (TransitionGroupDocNode) nodeTranGroup.ChangeChildren(
nodeTranGroup.Children.ToList().ConvertAll(nodeTran => nodeTran.CopyId()));
}
return (DocNode) nodeTranGroup;
})).ChangeAutoManageChildren(false)).ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
// If this PeptideDocNode is already a child of the PeptideGroupDocNode,
// ignore it.
if (peptideGroupDocNode.Children.Contains(nodePep => Equals(((PeptideDocNode) nodePep).Key, newNodePep.Key)))
{
Console.WriteLine(Resources.ViewLibraryPepMatching_AddProteomePeptides_Skipping__0__already_present, newNodePep.Peptide.Sequence);
continue;
}
// Otherwise, add it to the list of children for the PeptideGroupNode.
var newChildren = peptideGroupDocNode.Children.Cast<PeptideDocNode>().ToList();
newChildren.Add(newNodePep);
newChildren.Sort(FastaSequence.ComparePeptides);
// Store modified proteins by global index in a HashSet for second pass.
var newPeptideGroupDocNode = peptideGroupDocNode.ChangeChildren(newChildren.Cast<DocNode>().ToArray())
.ChangeAutoManageChildren(false);
// If the protein was already in the document, replace with the new PeptideGroupDocNode.
if (foundInDoc)
document = (SrmDocument)document.ReplaceChild(newPeptideGroupDocNode);
// Otherwise, update the list of new PeptideGroupDocNodes to add.
else
{
if (foundInList)
dictPeptideGroupsNew.Remove(peptideGroupDocNode.Name);
dictPeptideGroupsNew.Add(peptideGroupDocNode.Name, (PeptideGroupDocNode) newPeptideGroupDocNode);
}
// If we are only adding a single node, select it.
if (PeptideMatches.Count == 1)
selectedPath = new IdentityPath(new[] {peptideGroupDocNode.Id, newNodePep.Peptide});
// If the user only wants to add the first protein found,
// we break the foreach loop after peptide has been added to its first protein.)
if (FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.FirstOccurence)
break;
}
}
if (dictPeptideGroupsNew.Count == 0)
{
return document;
}
// Sort the peptides.
var nodePepGroupsSortedChildren = new List<PeptideGroupDocNode>();
foreach(PeptideGroupDocNode nodePepGroup in dictPeptideGroupsNew.Values)
{
var newChildren = nodePepGroup.Children.ToList();
// Have to cast all children to PeptideDocNodes in order to sort.
var newChildrenNodePeps = newChildren.Cast<PeptideDocNode>().ToList();
newChildrenNodePeps.Sort(FastaSequence.ComparePeptides);
nodePepGroupsSortedChildren.Add((PeptideGroupDocNode)
nodePepGroup.ChangeChildren(newChildrenNodePeps.Cast<DocNode>().ToArray()));
}
// Sort the proteins.
nodePepGroupsSortedChildren.Sort((node1, node2) => Comparer<string>.Default.Compare(node1.Name, node2.Name));
IdentityPath selPathTemp = selectedPath, nextAdd;
document = document.AddPeptideGroups(nodePepGroupsSortedChildren, false,
toPath, out selectedPath, out nextAdd);
selectedPath = PeptideMatches.Count == 1 ? selPathTemp : selectedPath;
return document;
}
public BackgroundWorker(MinimizeResultsDlg dlg, ILongWaitBroker longWaitBroker)
{
_dlg = dlg;
_longWaitBroker = longWaitBroker;
}
private void DownloadTools(ILongWaitBroker waitBroker,
IEnumerable<ToolUpdateInfo> tools,
out ICollection<ToolUpdateInfo> successfulDownloads,
out ICollection<string> failedDownloads)
{
successfulDownloads = new Collection<ToolUpdateInfo>();
failedDownloads = new Collection<string>();
ToolDir = Directory.CreateDirectory(Path.Combine(Path.GetTempPath(), "ToolDir")); // Not L10N
foreach (var tool in tools)
{
var individualDir = Directory.CreateDirectory(Path.Combine(ToolDir.FullName, tool._packageName));
try
{
tool.FilePath = _updateHelper.GetToolZipFile(waitBroker, tool._packageIdentifer, individualDir.FullName);
successfulDownloads.Add(tool);
}
catch (ToolExecutionException)
{
failedDownloads.Add(tool._packageName);
}
}
}
public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, ref TransitionGroupDocNode nodeTranGroup,
int resultsIndex, int?resultsFile, bool subsequent, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
PeakMatchData referenceTarget;
PeakMatchData[] referenceMatchData;
DateTime? runTime;
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out referenceTarget, out referenceMatchData, out runTime);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
for (int j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (!resultsFile.HasValue || resultsFile.Value == j)) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
{
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return(doc);
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
var client = ToolStoreUtil.CreateClient();
return client.GetToolZipFile(waitBroker, packageIdentifier, directory);
}
public string GetToolZipFile(ILongWaitBroker waitBroker, string packageIdentifier, string directory)
{
if (FailDownload)
throw new ToolExecutionException(Resources.TestToolStoreClient_GetToolZipFile_Error_downloading_tool);
if (TestDownloadPath != null)
return TestDownloadPath;
foreach (var item in ToolStoreItems ?? GetToolStoreItems())
{
if (item.Identifier.Equals(packageIdentifier))
{
string fileName = Path.GetFileName(item.FilePath);
if (fileName == null)
throw new ToolExecutionException(Resources.TestToolStoreClient_GetToolZipFile_Error_downloading_tool);
string path = Path.Combine(directory, fileName);
File.Copy(item.FilePath, path, true);
return path;
}
}
throw new ToolExecutionException(Resources.TestToolStoreClient_GetToolZipFile_Cannot_find_a_file_with_that_identifier_);
}
private static SrmDocument AddPeptidesToLibraryGroup(SrmDocument document,
ICollection<PeptideMatch> listMatches,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = listMatches.Count;
var listPeptides = new List<PeptideDocNode>();
foreach (var match in listMatches)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = null;
return document;
}
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
listPeptides.Add(match.NodePep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL));
}
bool hasVariable =
listPeptides.Contains(nodePep => nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods);
// Use existing group by this name, if present.
var nodePepGroupNew = FindPeptideGroupDocNode(document, Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides);
if(nodePepGroupNew != null)
{
var newChildren = nodePepGroupNew.Children.ToList();
newChildren.AddRange(listPeptides.ConvertAll(nodePep => (DocNode) nodePep));
selectedPath = (listPeptides.Count == 1 ? new IdentityPath(nodePepGroupNew.Id, listPeptides[0].Id) : toPath);
nodePepGroupNew = (PeptideGroupDocNode) nodePepGroupNew.ChangeChildren(newChildren);
if (hasVariable)
nodePepGroupNew = (PeptideGroupDocNode) nodePepGroupNew.ChangeAutoManageChildren(false);
return (SrmDocument) document.ReplaceChild(nodePepGroupNew);
}
else
{
nodePepGroupNew = new PeptideGroupDocNode(new PeptideGroup(),
Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides,
string.Empty, listPeptides.ToArray());
if (hasVariable)
nodePepGroupNew = (PeptideGroupDocNode) nodePepGroupNew.ChangeAutoManageChildren(false);
IdentityPath nextAdd;
document = document.AddPeptideGroups(new[] { nodePepGroupNew }, true,
toPath, out selectedPath, out nextAdd);
selectedPath = new IdentityPath(selectedPath, nodePepGroupNew.Children[0].Id);
return document;
}
}
private static void FindInputFiles(string dir, ICollection <string> inputFiles, ILongWaitBroker broker)
{
broker.ProgressValue = 0;
FindInputFiles(dir, inputFiles, broker, 0, 100);
}
/// <summary>
/// Tries to match each library peptide to document settings.
/// </summary>
public void MatchAllPeptides(ILongWaitBroker broker)
{
_chargeSettingsMap = new SrmSettings[128];
// Build a dictionary mapping sequence to proteins because getting this information is slow.
var dictSequenceProteins = new Dictionary<string, IList<ProteinInfo>>();
var dictNewNodePeps = new Dictionary<PeptideSequenceModKey, PeptideMatch>();
PeptideMatches = null;
MatchedPeptideCount = 0;
int peptides = 0;
int totalPeptides = _libraryPepInfos.Length;
foreach (ViewLibraryPepInfo pepInfo in _libraryPepInfos)
{
if (broker.IsCanceled)
return;
int charge = pepInfo.Key.Charge;
// Find the matching peptide.
var nodePepMatched = AssociateMatchingPeptide(pepInfo, charge).PeptideNode;
if (nodePepMatched != null)
{
MatchedPeptideCount++;
PeptideMatch peptideMatchInDict;
// If peptide is already in the dictionary of peptides to add, merge the children.
if (!dictNewNodePeps.TryGetValue(nodePepMatched.SequenceKey, out peptideMatchInDict))
{
IList<ProteinInfo> matchedProteins = null;
var sequence = nodePepMatched.Peptide.Sequence;
// This is only set if the user has checked the associate peptide box.
if (_backgroundProteome != null)
{
// We want to query the background proteome as little as possible,
// so sequences are mapped to protein lists in a dictionary.
if (!dictSequenceProteins.TryGetValue(sequence, out matchedProteins))
{
using (var proteomeDb = _backgroundProteome.OpenProteomeDb())
{
var digestion = _backgroundProteome.GetDigestion(proteomeDb, Settings.PeptideSettings);
if (digestion != null)
{
matchedProteins = digestion.GetProteinsWithSequence(sequence).Select(protein=>new ProteinInfo(protein)).ToList();
dictSequenceProteins.Add(sequence, matchedProteins);
}
}
}
}
dictNewNodePeps.Add(nodePepMatched.SequenceKey,
new PeptideMatch(nodePepMatched, matchedProteins,
MatchesFilter(sequence, charge)));
}
else
{
PeptideDocNode nodePepInDictionary = peptideMatchInDict.NodePep;
if (!nodePepInDictionary.HasChildCharge(charge))
{
List<DocNode> newChildren = nodePepInDictionary.Children.ToList();
newChildren.AddRange(nodePepMatched.Children);
newChildren.Sort(Peptide.CompareGroups);
var key = nodePepMatched.SequenceKey;
dictNewNodePeps.Remove(key);
dictNewNodePeps.Add(key,
new PeptideMatch((PeptideDocNode)nodePepInDictionary.ChangeChildren(newChildren),
peptideMatchInDict.Proteins, peptideMatchInDict.MatchesFilterSettings));
}
}
}
peptides++;
int progressValue = (int)((peptides + 0.0) / totalPeptides * PERCENT_PEPTIDE_MATCH);
broker.ProgressValue = progressValue;
}
PeptideMatches = dictNewNodePeps;
}
public void PerformWork(ILongWaitBroker broker)
{
_performWork();
}
private void DownloadR(ILongWaitBroker longWaitBroker)
{
// the repository containing the downloadable R exes
const string baseUri = "http://cran.r-project.org/bin/windows/base/"; // Not L10N
// format the file name, e.g. R-2.15.2-win.exe
string exe = "R-" + _version + "-win.exe"; // Not L10N
// create the download path for the file
DownloadPath = Path.GetTempPath() + exe;
// create the webclient
using (var webClient = TestDownloadClient ?? new MultiFileAsynchronousDownloadClient(longWaitBroker, 2))
{
// First try downloading it as if it is the most recent release of R. The most
// recent version is stored in a different location of the CRAN repo than older versions.
// Otherwise, check and see if it is an older release
var recentUri = new Uri(baseUri + exe);
var olderUri = new Uri(baseUri + "old/" + _version + "/" + exe); // Not L10N
if (!webClient.DownloadFileAsync(recentUri, DownloadPath) && !webClient.DownloadFileAsync(olderUri, DownloadPath))
throw new ToolExecutionException(
TextUtil.LineSeparate(
Resources.RInstaller_DownloadR_Download_failed_,
Resources
.RInstaller_DownloadPackages_Check_your_network_connection_or_contact_the_tool_provider_for_installation_support_));
}
}
public void PerformWork(ILongWaitBroker broker)
{
_broker = broker;
_performWork(this);
}
/// <summary>
/// Adds a list of PeptideDocNodes found in the library to the current document.
/// </summary>
public SrmDocument AddPeptides(SrmDocument document, ILongWaitBroker broker, IdentityPath toPath, out IdentityPath selectedPath)
{
if (toPath != null &&
toPath.Depth == (int)SrmDocument.Level.MoleculeGroups &&
ReferenceEquals(toPath.GetIdentity((int)SrmDocument.Level.MoleculeGroups), SequenceTree.NODE_INSERT_ID))
{
toPath = null;
}
SkippedPeptideCount = 0;
var dictCopy = new Dictionary<PeptideSequenceModKey, PeptideMatch>();
// Make heavy mods explicit
if (PeptideMatches.Values.Contains(match => match.NodePep.HasExplicitMods
&& match.NodePep.ExplicitMods.HeavyModifications != null))
{
_matcher.ConvertAllHeavyModsExplicit();
}
// Call ensure mods on all peptides to be added to the document.
var listDefStatMods = new MappedList<string, StaticMod>();
listDefStatMods.AddRange(Properties.Settings.Default.StaticModList);
listDefStatMods.AddRange(document.Settings.PeptideSettings.Modifications.StaticModifications);
var listDefHeavyMods = new MappedList<string, StaticMod>();
listDefHeavyMods.AddRange(Properties.Settings.Default.HeavyModList);
listDefHeavyMods.AddRange(document.Settings.PeptideSettings.Modifications.HeavyModifications);
foreach (var key in PeptideMatches.Keys)
{
var match = PeptideMatches[key];
var nodePepDocSet = match.NodePep;
if (_matcher.MatcherPepMods != null)
nodePepDocSet = match.NodePep.EnsureMods(_matcher.MatcherPepMods,
document.Settings.PeptideSettings.Modifications,
listDefStatMods, listDefHeavyMods);
if (!dictCopy.ContainsKey(nodePepDocSet.SequenceKey))
dictCopy.Add(nodePepDocSet.SequenceKey,
new PeptideMatch(nodePepDocSet, match.Proteins,
match.MatchesFilterSettings));
}
if (!Properties.Settings.Default.LibraryPeptidesKeepFiltered)
{
// TODO: This removes entire peptides where only a single
// precursor does not match. e.g. the library contains
// a singly charged precursor match, but also doubly charged
dictCopy = dictCopy.Where(match => match.Value.MatchesFilterSettings)
.ToDictionary(match => match.Key, match => match.Value);
}
SrmDocument newDocument = UpdateExistingPeptides(document, dictCopy, toPath, out selectedPath);
toPath = selectedPath;
// If there is an associated background proteome, add peptides that can be
// matched to the proteins from the background proteom.
if (_backgroundProteome != null)
{
newDocument = AddProteomePeptides(newDocument, dictCopy, broker,
toPath, out selectedPath);
}
toPath = selectedPath;
// Add all remaining peptides as a peptide list.
if (_backgroundProteome == null || Properties.Settings.Default.LibraryPeptidesAddUnmatched)
{
var listPeptidesToAdd = dictCopy.Values.ToList();
listPeptidesToAdd.RemoveAll(match => match.Proteins != null && match.Proteins.Count > 0);
if (listPeptidesToAdd.Count > 0)
{
newDocument = AddPeptidesToLibraryGroup(newDocument, listPeptidesToAdd, broker,
toPath, out selectedPath);
}
}
return newDocument;
}
// Consider: the location of the following python links is assumed to be relatively stable, but could change. We
// might want to package these scripts with Skyline itself to assure that they are available
private void DownloadPip(ILongWaitBroker longWaitBroker)
{
// location of the setuptools install script
const string setupToolsScript = "https://bitbucket.org/pypa/setuptools/downloads/ez_setup.py"; // Not L10N
SetupToolsPath = Path.GetTempPath() + "ez_setup.py"; // Not L10N
// location of the pip install script
const string pipScript = "https://raw.github.com/pypa/pip/master/contrib/get-pip.py"; // Not L10N
PipPath = Path.GetTempPath() + "get-pip.py"; // Not L10N
using (var webClient = TestPipDownloadClient ?? new MultiFileAsynchronousDownloadClient(longWaitBroker, 2))
{
if (!webClient.DownloadFileAsync(new Uri(setupToolsScript), SetupToolsPath) ||
!webClient.DownloadFileAsync(new Uri(pipScript), PipPath))
{
throw new ToolExecutionException(Resources.PythonInstaller_DownloadPip_Download_failed__Check_your_network_connection_or_contact_Skyline_developers_);
}
}
}
/// <summary>
/// Matches library peptides to the current document settings and adds them to the document.
/// This needs to be one function so that we can use one LongWaitDlg.
/// </summary>
public void AddAllPeptidesToDocument(ILongWaitBroker broker)
{
MatchAllPeptides(broker);
if (broker.IsCanceled)
return;
if (MatchedPeptideCount == 0)
return;
if (broker.ShowDialog(EnsureDuplicateProteinFilter) == DialogResult.Cancel)
return;
IdentityPath selectedPath;
IdentityPath toPath = AddAllPeptidesSelectedPath;
DocAllPeptides = AddPeptides(_document, broker, toPath, out selectedPath);
AddAllPeptidesSelectedPath = selectedPath;
}
private IEnumerable<string> DownloadPackages(ILongWaitBroker waitBroker, IEnumerable<string> packagesToDownload)
{
ICollection<string> downloadPaths = new Collection<string>();
ICollection<string> failedDownloads = new Collection<string>();
using (var webClient = TestDownloadClient ?? new MultiFileAsynchronousDownloadClient(waitBroker, PackageUris.Count))
{
foreach (var package in packagesToDownload)
{
Match file = Regex.Match(package, @"[^/]*$"); // Not L10N
string downloadPath = Path.GetTempPath() + file;
if (webClient.DownloadFileAsync(new Uri(package), downloadPath))
{
downloadPaths.Add(downloadPath);
}
else
{
failedDownloads.Add(package);
}
}
}
if (failedDownloads.Count != 0)
{
throw new ToolExecutionException(
TextUtil.LineSeparate(
Resources.PythonInstaller_DownloadPackages_Failed_to_download_the_following_packages_,
string.Empty,
TextUtil.LineSeparate(failedDownloads),
string.Empty,
Resources.PythonInstaller_DownloadPython_Check_your_network_connection_or_contact_the_tool_provider_for_installation_support_));
}
return downloadPaths;
}
private void QueryPeptideProteins(ILongWaitBroker longWaitBroker)
{
List<HashSet<Protein>> peptideProteins = new List<HashSet<Protein>>();
if (BackgroundProteome != null)
{
using (var proteomeDb = BackgroundProteome.OpenProteomeDb())
{
Digestion digestion = BackgroundProteome.GetDigestion(proteomeDb, SrmDocument.Settings.PeptideSettings);
foreach (var peptideDocNode in _peptideDocNodes)
{
HashSet<Protein> proteins = new HashSet<Protein>();
if (digestion != null)
{
if (longWaitBroker.IsCanceled)
{
return;
}
foreach (Protein protein in digestion.GetProteinsWithSequence(peptideDocNode.Peptide.Sequence))
{
if (protein.Sequence == PeptideGroupDocNode.PeptideGroup.Sequence)
{
_targetIsInBackgroundProteome = true;
continue;
}
proteins.Add(protein);
}
}
peptideProteins.Add(proteins);
}
}
}
_peptideProteins = peptideProteins;
}
private void BeginUpdate(ILongWaitBroker broker)
{
AppDeployment.UpdateAsync(ev => update_ProgressChanged(ev, broker), update_Complete);
}
private void OptimizeCache(string fileName, ILongWaitBroker progress)
{
// Optimize the results cache to get rid of any unnecessary
// chromatogram data.
var settings = Document.Settings;
if (settings.HasResults)
{
var results = settings.MeasuredResults;
if (results.IsLoaded)
{
var resultsNew = results.OptimizeCache(fileName, _chromatogramManager.StreamManager, progress);
if (!ReferenceEquals(resultsNew, results))
{
SrmDocument docNew, docCurrent;
do
{
docCurrent = Document;
docNew = docCurrent.ChangeMeasuredResults(resultsNew);
}
while (!SetDocument(docNew, docCurrent));
}
}
}
else
{
string cachePath = ChromatogramCache.FinalPathForName(DocumentFilePath, null);
FileEx.SafeDelete(cachePath, true);
}
}
private static void CopyOldTools(string outerToolsFolderPath, ILongWaitBroker broker)
{
//Copy tools to a different folder then Directory.Move if successful.
string tempOuterToolsFolderPath = string.Concat(outerToolsFolderPath, "_installing"); // Not L10N
if (Directory.Exists(tempOuterToolsFolderPath))
{
DirectoryEx.SafeDelete(tempOuterToolsFolderPath);
// Not sure this is necessay, but just to be safe
if (Directory.Exists(tempOuterToolsFolderPath))
throw new Exception(Resources.Program_CopyOldTools_Error_copying_external_tools_from_previous_installation);
}
// Must create the tools directory to avoid ending up here again next time
Directory.CreateDirectory(tempOuterToolsFolderPath);
ToolList toolList = Settings.Default.ToolList;
int numTools = toolList.Count;
const int endValue = 100;
int progressValue = 0;
int increment = (endValue - progressValue)/(numTools +1);
foreach (var tool in toolList)
{
string toolDirPath = tool.ToolDirPath;
if (!string.IsNullOrEmpty(toolDirPath) && Directory.Exists(toolDirPath))
{
string foldername = Path.GetFileName(toolDirPath);
string newDir = Path.Combine(outerToolsFolderPath, foldername);
string tempNewDir = Path.Combine(tempOuterToolsFolderPath, foldername);
if (!Directory.Exists(tempNewDir))
DirectoryEx.DirectoryCopy(toolDirPath, tempNewDir, true);
tool.ToolDirPath = newDir; // Update the tool to point to its new directory.
tool.ArgsCollectorDllPath = tool.ArgsCollectorDllPath.Replace(toolDirPath, newDir);
}
if (broker.IsCanceled)
{
// Don't leave around a corrupted directory
DirectoryEx.SafeDelete(tempOuterToolsFolderPath);
return;
}
progressValue += increment;
broker.ProgressValue = progressValue;
}
Directory.Move(tempOuterToolsFolderPath, outerToolsFolderPath);
Settings.Default.ToolList = ToolList.CopyTools(toolList);
}
/// <summary>
/// The asynchronous download client links a webClient to a LongWaitBroker. It supports
/// multiple asynchronous downloads, and updates the associated broker's progress value.
/// </summary>
/// <param name="waitBroker">The associated LongWaitBroker</param>
/// <param name="files">The numbers of file this instance is expected to download. This
/// is used to accurately update the broker's progress value</param>
public MultiFileAsynchronousDownloadClient(ILongWaitBroker waitBroker, int files)
{
_longWaitBroker = waitBroker;
_webClient = new WebClient();
FilesDownloaded = 0;
_webClient.DownloadProgressChanged += (sender, args) =>
{
_longWaitBroker.ProgressValue = (int) Math.Min(100, ((((double) FilesDownloaded)/files)*100)
+ ((1.0/files)*args.ProgressPercentage));
};
_webClient.DownloadFileCompleted += (sender, args) =>
{
FilesDownloaded++;
DownloadSucceeded = (args.Error == null);
DownloadComplete = true;
};
}
public BackgroundWorker(MinimizeResultsDlg dlg, ILongWaitBroker longWaitBroker)
{
_dlg = dlg;
_longWaitBroker = longWaitBroker;
}
private void FindDataFiles(string directory, bool overwrite, ILongWaitBroker longWaitBroker)
{
// Don't search if every spectrum source file has an exact match and an alternate match
if (directory == null || !Directory.Exists(directory) || (!overwrite && SpectrumSourceFiles.Values.All(s => s.HasMatches)))
return;
if (longWaitBroker != null)
{
longWaitBroker.Message =
string.Format(Resources.ImportResultsControl_FindResultsFiles_Searching_for_matching_results_files_in__0__, directory);
}
try
{
foreach (string entry in Directory.EnumerateFileSystemEntries(directory))
{
if (longWaitBroker != null && longWaitBroker.IsCanceled)
return;
if (entry != null && DataSourceUtil.IsDataSource(entry))
TryMatch(entry, overwrite);
}
}
// ReSharper disable once EmptyGeneralCatchClause
catch (Exception)
{
// No permissions on folder
}
}
