public void MinimizeToFile(string targetFile, CacheFormat cacheFormat)
{
var targetSkydFile = ChromatogramCache.FinalPathForName(targetFile, null);
using (var skydSaver = new FileSaver(targetSkydFile, true))
using (var scansSaver = new FileSaver(targetSkydFile + ChromatogramCache.SCANS_EXT, true))
using (var peaksSaver = new FileSaver(targetSkydFile + ChromatogramCache.PEAKS_EXT, true))
using (var scoreSaver = new FileSaver(targetSkydFile + ChromatogramCache.SCORES_EXT, true))
{
var minimizer = Document.Settings.MeasuredResults.GetChromCacheMinimizer(Document);
var settings = new ChromCacheMinimizer.Settings().ChangeCacheFormat(cacheFormat);
var lockObject = new object();
ProgressMonitor.UpdateProgress(_progressStatus = _progressStatus.ChangeMessage(Resources.SrmDocumentSharing_MinimizeToFile_Writing_chromatograms));
minimizer.Minimize(settings, stats =>
{
if (ProgressMonitor.IsCanceled)
{
throw new OperationCanceledException();
}
lock (lockObject)
{
ProgressMonitor.UpdateProgress(_progressStatus = _progressStatus.ChangePercentComplete(stats.PercentComplete));
}
}, skydSaver.FileStream, scansSaver.FileStream, peaksSaver.FileStream, scoreSaver.FileStream);
skydSaver.Commit();
}
}
public IrtDb AddPeptides(IProgressMonitor monitor, IList <DbIrtPeptide> newPeptides, ref IProgressStatus status)
{
var total = newPeptides.Count;
var i = 0;
using (var session = OpenWriteSession())
using (var transaction = session.BeginTransaction())
{
foreach (var peptideNewDisconnected in newPeptides.Select(peptideNew => new DbIrtPeptide(peptideNew)
{
Id = null
}))
{
session.SaveOrUpdate(peptideNewDisconnected);
if (monitor != null)
{
if (monitor.IsCanceled)
{
return(null);
}
monitor.UpdateProgress(status = status.ChangePercentComplete(++i * 100 / total));
}
}
transaction.Commit();
}
if (monitor != null)
{
monitor.UpdateProgress(status.Complete());
}
return(ChangeProp(ImClone(this), im => im.LoadPeptides(newPeptides)));
}
private static bool UpdatePrecentComplete(IProgressMonitor progressMonitor, int percentComplete,
ref IProgressStatus progressStatus)
{
if (progressMonitor.IsCanceled)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return(false);
}
if (progressStatus.PercentComplete != percentComplete)
{
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(percentComplete));
}
return(true);
}
private bool UpdateProgress(int totalPeptideCount, int doneCount)
{
if (ProgressMonitor != null)
{
if (ProgressMonitor.IsCanceled)
{
return(false);
}
int progressValue = (doneCount) * 100 / totalPeptideCount;
ProgressMonitor.UpdateProgress(_progressStatus = _progressStatus.ChangePercentComplete(progressValue));
}
return(true);
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref IProgressStatus status, TextWriter writer)
{
if (shouldCancel)
{
status.Cancel();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(stringToWriteToWriter))
{
writer.WriteLine(stringToWriteToWriter);
}
status.ChangePercentComplete(100);
progress.UpdateProgress(status);
}
public bool Export(CancellationToken cancellationToken, IProgressMonitor progressMonitor, ref IProgressStatus status, ViewInfo viewInfo, TextWriter writer, DsvWriter dsvWriter)
{
progressMonitor = progressMonitor ?? new SilentProgressMonitor();
using (var bindingListSource = new BindingListSource(cancellationToken))
{
bindingListSource.SetViewContext(this, viewInfo);
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(5)
.ChangeMessage(Resources.ExportReportDlg_ExportReport_Writing_report));
WriteDataWithStatus(progressMonitor, ref status, writer, bindingListSource, dsvWriter);
if (progressMonitor.IsCanceled)
{
return(false);
}
writer.Flush();
progressMonitor.UpdateProgress(status = status.Complete());
}
return(true);
}
private void SrmDocumentSharing_SaveProgress(object sender, SaveProgressEventArgs e)
{
if (ProgressMonitor != null)
{
if (ProgressMonitor.IsCanceled)
{
e.Cancel = true;
return;
}
// TODO: More accurate total byte progress
double percentCompressed = (e.TotalBytesToTransfer > 0 ?
1.0 * e.BytesTransferred / e.TotalBytesToTransfer : 0);
int progressValue = (int)Math.Round((EntriesSaved + percentCompressed) * 100 / CountEntries);
if (progressValue != _progressStatus.PercentComplete)
{
_progressStatus = _progressStatus.ChangePercentComplete(progressValue);
if (e.CurrentEntry == null)
{
ProgressMonitor.UpdateProgress(_progressStatus = _progressStatus.ChangeMessage(DefaultMessage));
}
else
{
if (!Equals(CurrentEntry, e.CurrentEntry.FileName))
{
if (CurrentEntry != null)
{
EntriesSaved++;
}
CurrentEntry = e.CurrentEntry.FileName;
}
var message = string.Format(Resources.SrmDocumentSharing_SrmDocumentSharing_SaveProgress_Compressing__0__,
e.CurrentEntry.FileName);
ProgressMonitor.UpdateProgress(_progressStatus = _progressStatus.ChangeMessage(message));
}
}
}
}
private bool Load(ILoadMonitor loader, IProgressStatus status, bool cached)
{
try
{
int loadPercent = 100;
if (!cached)
{
// Building the cache will take 95% of the load time.
loadPercent = 5;
status = status.ChangeMessage(string.Format(Resources.XHunterLibrary_Load_Building_binary_cache_for__0__library, Path.GetFileName(FilePath)));
status = status.ChangePercentComplete(0);
loader.UpdateProgress(status);
if (!CreateCache(loader, status, 100 - loadPercent))
{
return(false);
}
}
status = status.ChangeMessage(string.Format(Resources.XHunterLibrary_Load_Loading__0__library, Path.GetFileName(FilePath)));
loader.UpdateProgress(status);
var valueCache = new ValueCache();
var sm = loader.StreamManager;
using (Stream stream = sm.CreateStream(CachePath, FileMode.Open, true))
{
// Read library header from the end of the cache
int countHeader = (int)LibHeaders.count * sizeof(int);
stream.Seek(-countHeader, SeekOrigin.End);
byte[] libHeader = new byte[countHeader];
ReadComplete(stream, libHeader, countHeader);
int version = GetInt32(libHeader, (int)LibHeaders.format_version);
if (version != FORMAT_VERSION_CACHE)
{
return(false);
}
int countRevisionBytes = GetInt32(libHeader, (int)LibHeaders.revision_byte_count);
int countIdBytes = GetInt32(libHeader, (int)LibHeaders.id_byte_count);
stream.Seek(-countHeader - countRevisionBytes - countIdBytes, SeekOrigin.End);
Revision = ReadString(stream, countRevisionBytes);
Id = ReadString(stream, countIdBytes);
int numSpectra = GetInt32(libHeader, (int)LibHeaders.num_spectra);
var libraryEntries = new XHunterSpectrumInfo[numSpectra];
// Seek to beginning of spectrum headers
long locationHeaders = BitConverter.ToInt64(libHeader,
((int)LibHeaders.location_headers_lo) * sizeof(int));
stream.Seek(locationHeaders, SeekOrigin.Begin);
for (int i = 0; i < numSpectra; i++)
{
int percent = (100 - loadPercent) + (i * loadPercent / numSpectra);
if (status.PercentComplete != percent)
{
// Check for cancellation after each integer change in percent loaded.
if (loader.IsCanceled)
{
loader.UpdateProgress(status.Cancel());
return(false);
}
// If not cancelled, update progress.
loader.UpdateProgress(status = status.ChangePercentComplete(percent));
}
// Read spectrum header
LibKey key = LibKey.Read(valueCache, stream);
long location = PrimitiveArrays.ReadOneValue <long>(stream);
float processedIntensity = PrimitiveArrays.ReadOneValue <float>(stream);
int numPeaks = PrimitiveArrays.ReadOneValue <int>(stream);
float expect = PrimitiveArrays.ReadOneValue <float>(stream);
libraryEntries[i] = new XHunterSpectrumInfo(key, processedIntensity, expect, (short)numPeaks, location);
}
// Checksum = checksum.ChecksumValue;
SetLibraryEntries(libraryEntries);
loader.UpdateProgress(status.Complete());
// Create the stream from which the spectra will be read
CreateStream(loader);
}
return(true);
}
catch (InvalidDataException x)
{
if (!cached)
{
loader.UpdateProgress(status.ChangeErrorException(x));
}
return(false);
}
catch (IOException x)
{
if (!cached)
{
loader.UpdateProgress(status.ChangeErrorException(x));
}
return(false);
}
catch (Exception x)
{
if (!cached)
{
x = new Exception(string.Format(Resources.XHunterLibrary_Load_Failed_loading_library__0__, FilePath), x);
loader.UpdateProgress(status.ChangeErrorException(x));
}
return(false);
}
finally
{
if (ReadStream != null)
{
// Close the read stream to ensure we never leak it.
// This only costs on extra open, the first time the
// active document tries to read.
try { ReadStream.CloseStream(); }
catch (IOException) { }
}
}
}
// ReSharper restore UnusedMember.Local
private bool CreateCache(ILoadMonitor loader, IProgressStatus status, int percent)
{
var sm = loader.StreamManager;
BufferedStream stream = new BufferedStream(CreateStream(loader), 32 * 1024);
int version = 1;
string id = string.Empty, revision = string.Empty;
int size = ReadSize(stream);
int i;
if (size == 0)
{
version = 2;
size = ReadSize(stream);
const int countLibHeader = 256 - 8;
byte[] libHeader = new byte[countLibHeader];
if (stream.Read(libHeader, 0, libHeader.Length) != libHeader.Length)
{
throw new InvalidDataException(Resources.XHunterLibrary_CreateCache_Data_truncation_in_library_header_File_may_be_corrupted);
}
for (i = 0; i < libHeader.Length; i++)
{
if (libHeader[i] == 0)
{
break;
}
}
string header = Encoding.UTF8.GetString(libHeader, 0, i);
Match match = REGEX_HEADER.Match(header);
if (match.Success)
{
version = int.Parse(match.Groups[1].Value);
id = match.Groups[2].Value;
revision = match.Groups[3].Value;
}
}
var setLibKeys = new HashSet <LibKey>(size);
var libraryEntries = new List <XHunterSpectrumInfo>(size);
const int countHeader = ((int)SpectrumHeaders2.count) * sizeof(int);
byte[] specHeader = new byte[1024];
byte[] specSequence = new byte[1024];
i = 0;
while (stream.Read(specHeader, 0, countHeader) == countHeader)
{
int percentComplete = (i++ *percent / size);
if (status.PercentComplete != percentComplete)
{
// Check for cancellation after each integer change in percent loaded.
if (loader.IsCanceled)
{
loader.UpdateProgress(status.Cancel());
return(false);
}
// If not cancelled, update progress.
loader.UpdateProgress(status = status.ChangePercentComplete(percentComplete));
}
int charge = (version == 1
? GetInt32(specHeader, ((int)SpectrumHeaders1.charge))
: GetInt32(specHeader, ((int)SpectrumHeaders2.charge)));
float i2 = (version == 1
? GetSingle(specHeader, ((int)SpectrumHeaders1.i2))
: GetSingle(specHeader, ((int)SpectrumHeaders2.i2)));
int seqLength = (version == 1
? GetInt32(specHeader, ((int)SpectrumHeaders1.seq_len))
: GetInt32(specHeader, ((int)SpectrumHeaders2.seq_len)));
float expect = (version == 1 ? 0.001f : GetSingle(specHeader, (int)SpectrumHeaders2.expect));
// Read sequence information
ReadComplete(stream, specSequence, seqLength);
specSequence[seqLength] = 0;
short numPeaks = (short)ReadSize(stream);
// Save spectrum location
long location = stream.Position;
// Read over spectrum
int countPeaks = (sizeof(byte) + sizeof(float)) * numPeaks;
stream.Seek(countPeaks, SeekOrigin.Current); // Skip spectrum
// Read modifications
int numMods = ReadSize(stream);
string modifiedSequence = Encoding.UTF8.GetString(specSequence, 0, seqLength);
if (numMods > 0)
{
StringBuilder sb = new StringBuilder();
ReadComplete(stream, specHeader, (4 + sizeof(double)) * numMods);
int iLast = 0;
double modTotal = 0;
for (int j = 0; j < numMods; j++)
{
int iPos = GetInt32(specHeader, j * 3);
double mod = BitConverter.ToDouble(specHeader, (j * 3 + 1) * 4);
// X! Hunter allows multiple modifications on the same
// residue. So, they need to be totaled, and assigned to a
// single residue to allow them to match Skyline modification
// settings.
if (iPos > iLast)
{
if (modTotal != 0)
{
sb.Append(SequenceMassCalc.GetModDiffDescription(modTotal));
}
sb.Append(Encoding.UTF8.GetString(specSequence, iLast, iPos - iLast));
modTotal = 0;
}
modTotal += mod;
iLast = iPos;
}
if (modTotal != 0)
{
sb.Append(SequenceMassCalc.GetModDiffDescription(modTotal));
}
sb.Append(Encoding.UTF8.GetString(specSequence, iLast, seqLength - iLast));
modifiedSequence = sb.ToString();
}
// Skip over homologs (list of protein IDs and start positions from a FASTA
// file used to generate the library)
int numHomologs = ReadSize(stream);
for (int j = 0; j < numHomologs; j++)
{
stream.Seek(ReadSize(stream) + 4, SeekOrigin.Current);
}
// These libraries should not have duplicates, but just in case.
// Apparently, GPM libraries do contain redundancies, as we found
// when a revision lost this test.
var key = new LibKey(modifiedSequence, charge);
if (setLibKeys.Add(key))
{
libraryEntries.Add(new XHunterSpectrumInfo(key, i2, expect, numPeaks, location));
}
}
libraryEntries = FilterInvalidLibraryEntries(ref status, libraryEntries);
using (FileSaver fs = new FileSaver(CachePath, sm))
using (Stream outStream = sm.CreateStream(fs.SafeName, FileMode.Create, true))
{
foreach (var info in libraryEntries)
{
info.Key.Write(outStream);
PrimitiveArrays.WriteOneValue(outStream, info.Location);
PrimitiveArrays.WriteOneValue(outStream, info.ProcessedIntensity);
PrimitiveArrays.WriteOneValue(outStream, info.NumPeaks);
PrimitiveArrays.WriteOneValue(outStream, info.Expect);
}
byte[] revisionBytes = Encoding.UTF8.GetBytes(revision);
outStream.Write(revisionBytes, 0, revisionBytes.Length);
byte[] idBytes = Encoding.UTF8.GetBytes(id);
outStream.Write(idBytes, 0, idBytes.Length);
outStream.Write(BitConverter.GetBytes(revisionBytes.Length), 0, sizeof(int));
outStream.Write(BitConverter.GetBytes(idBytes.Length), 0, sizeof(int));
outStream.Write(BitConverter.GetBytes(FORMAT_VERSION_CACHE), 0, sizeof(int));
outStream.Write(BitConverter.GetBytes(libraryEntries.Count), 0, sizeof(int));
outStream.Write(BitConverter.GetBytes((long)0), 0, sizeof(long));
sm.Finish(outStream);
fs.Commit();
sm.SetCache(FilePath, CachePath);
}
loader.UpdateProgress(status.Complete());
return(true);
}
public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, ref IProgressStatus status, TextWriter writer)
{
// Make sure required streams are redirected.
psi.RedirectStandardOutput = true;
psi.RedirectStandardError = true;
_messageLog.Clear();
var proc = Process.Start(psi);
if (proc == null)
{
throw new IOException(string.Format(@"Failure starting {0} command.", psi.FileName));
}
if (stdin != null)
{
try
{
proc.StandardInput.Write(stdin);
}
finally
{
proc.StandardInput.Close();
}
}
var reader = new ProcessStreamReader(proc);
StringBuilder sbError = new StringBuilder();
int percentLast = 0;
string line;
while ((line = reader.ReadLine(progress)) != null)
{
if (writer != null && !line.StartsWith(HideLinePrefix))
{
writer.WriteLine(line);
}
if (progress == null || line.ToLowerInvariant().StartsWith(@"error"))
{
sbError.AppendLine(line);
}
else // if (progress != null)
{
if (progress.IsCanceled)
{
proc.Kill();
progress.UpdateProgress(status = status.Cancel());
return;
}
if (!string.IsNullOrEmpty(MessagePrefix) && line.StartsWith(MessagePrefix))
{
_messageLog.Add(line.Substring(MessagePrefix.Length));
}
else if (line.EndsWith(@"%"))
{
double percent;
string[] parts = line.Split(' ');
string percentPart = parts[parts.Length - 1];
if (double.TryParse(percentPart.Substring(0, percentPart.Length - 1), out percent))
{
percentLast = (int)percent;
status = status.ChangePercentComplete(percentLast);
if (percent >= 100 && status.SegmentCount > 0)
{
status = status.NextSegment();
}
progress.UpdateProgress(status);
}
}
else if (StatusPrefix == null || line.StartsWith(StatusPrefix))
{
// Remove prefix, if there is one.
if (StatusPrefix != null)
{
line = line.Substring(StatusPrefix.Length);
}
status = status.ChangeMessage(line);
progress.UpdateProgress(status);
}
}
}
proc.WaitForExit();
int exit = proc.ExitCode;
if (exit != 0)
{
line = proc.StandardError.ReadLine();
if (line != null)
{
sbError.AppendLine(line);
}
if (sbError.Length == 0)
{
sbError.AppendLine(@"Error occurred running process.");
}
string processPath = Path.GetDirectoryName(psi.FileName)?.Length == 0
? Path.Combine(Environment.CurrentDirectory, psi.FileName)
: psi.FileName;
// ReSharper disable LocalizableElement
sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}", processPath,
// ReSharper restore LocalizableElement
string.Join(" ", proc.StartInfo.Arguments), psi.WorkingDirectory,
stdin != null ? "\r\nStandard input:\r\n" + stdin : "");
throw new IOException(sbError.ToString());
}
// Make to complete the status, if the process succeeded, but never
// printed 100% to the console
if (percentLast < 100)
{
status = status.ChangePercentComplete(100);
if (status.SegmentCount > 0)
{
status = status.NextSegment();
}
if (progress != null)
{
progress.UpdateProgress(status);
}
}
}
public override Uri SendZipFile(Server server, string folderPath, string zipFilePath, IProgressMonitor progressMonitor)
{
_progressMonitor = progressMonitor;
_progressStatus = new ProgressStatus(String.Empty);
var zipFileName = Path.GetFileName(zipFilePath) ?? string.Empty;
// Upload zip file to pipeline folder.
using (_webClient = new NonStreamBufferingWebClient())
{
_webClient.UploadProgressChanged += webClient_UploadProgressChanged;
_webClient.UploadFileCompleted += webClient_UploadFileCompleted;
_webClient.Headers.Add(HttpRequestHeader.Authorization, server.AuthHeader);
var webDav = PanoramaUtil.Call(server.URI, "pipeline", folderPath, "getPipelineContainer", true); // Not L10N
var webDavInfo = _webClient.UploadString(webDav, PanoramaUtil.FORM_POST, string.Empty);
JObject jsonWebDavInfo = JObject.Parse(webDavInfo);
string webDavUrl = (string)jsonWebDavInfo["webDavURL"]; // Not L10N
// Upload Url minus the name of the zip file.
var baseUploadUri = new Uri(server.URI, webDavUrl);
// Use Uri.EscapeDataString instead of Uri.EscapleUriString.
// The latter will not escape characters such as '+' or '#'
var escapedZipFileName = Uri.EscapeDataString(zipFileName);
var tmpUploadUri = new Uri(baseUploadUri, escapedZipFileName + ".part"); // Not L10N
var uploadUri = new Uri(baseUploadUri, escapedZipFileName);
lock (this)
{
// Write to a temp file first. This will be renamed after a successful upload or deleted if the upload is canceled.
// Add a "Temporary" header so that LabKey marks this as a temporary file.
// https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=19220
_webClient.Headers.Add("Temporary", "T"); // Not L10N
_webClient.UploadFileAsync(tmpUploadUri, "PUT", zipFilePath); // Not L10N
// Wait for the upload to complete
Monitor.Wait(this);
}
if (progressMonitor.IsCanceled)
{
// Delete the temporary file on the server
progressMonitor.UpdateProgress(
_progressStatus =
_progressStatus.ChangeMessage(
Resources.WebPanoramaPublishClient_SendZipFile_Deleting_temporary_file_on_server));
DeleteTempZipFile(tmpUploadUri, server.AuthHeader);
return(null);
}
// Make sure the temporary file was uploaded to the server
ConfirmFileOnServer(tmpUploadUri, server.AuthHeader);
// Rename the temporary file
_progressStatus = _progressStatus.ChangeMessage(
Resources.WebPanoramaPublishClient_SendZipFile_Renaming_temporary_file_on_server);
progressMonitor.UpdateProgress(_progressStatus);
RenameTempZipFile(tmpUploadUri, uploadUri, server.AuthHeader);
_progressStatus = _progressStatus.ChangeMessage(Resources.WebPanoramaPublishClient_SendZipFile_Waiting_for_data_import_completion___);
progressMonitor.UpdateProgress(_progressStatus = _progressStatus.ChangePercentComplete(-1));
// Data must be completely uploaded before we can import.
Uri importUrl = PanoramaUtil.Call(server.URI, "targetedms", folderPath, "skylineDocUploadApi"); // Not L10N
// Need to tell server which uploaded file to import.
var dataImportInformation = new NameValueCollection
{
// For now, we only have one root that user can upload to
{ "path", "./" }, // Not L10N
{ "file", zipFileName } // Not L10N
};
byte[] responseBytes = _webClient.UploadValues(importUrl, PanoramaUtil.FORM_POST, dataImportInformation); // Not L10N
string response = Encoding.UTF8.GetString(responseBytes);
JToken importResponse = JObject.Parse(response);
// ID to check import status.
var details = importResponse["UploadedJobDetails"]; // Not L10N
int rowId = (int)details[0]["RowId"]; // Not L10N
Uri statusUri = PanoramaUtil.Call(server.URI, "query", folderPath, "selectRows", // Not L10N
"query.queryName=job&schemaName=pipeline&query.rowId~eq=" + rowId); // Not L10N
bool complete = false;
// Wait for import to finish before returning.
Uri result = null;
while (!complete)
{
if (progressMonitor.IsCanceled)
{
return(null);
}
string statusResponse = _webClient.UploadString(statusUri, PanoramaUtil.FORM_POST, string.Empty);
JToken jStatusResponse = JObject.Parse(statusResponse);
JToken rows = jStatusResponse["rows"]; // Not L10N
var row = rows.FirstOrDefault(r => (int)r["RowId"] == rowId); // Not L10N
if (row == null)
{
continue;
}
string status = (string)row["Status"]; // Not L10N
result = new Uri(server.URI, (string)row["_labkeyurl_Description"]); // Not L10N
if (string.Equals(status, "ERROR")) // Not L10N
{
var jobUrl = new Uri(server.URI, (string)row["_labkeyurl_RowId"]); // Not L10N
var e = new PanoramaImportErrorException(server.URI, jobUrl);
progressMonitor.UpdateProgress(
_progressStatus = _progressStatus.ChangeErrorException(e));
throw e;
}
complete = string.Equals(status, "COMPLETE"); // Not L10N
}
progressMonitor.UpdateProgress(_progressStatus.Complete());
return(result);
}
}
private bool Load(ILoadMonitor loader, IProgressStatus status, bool cached)
{
try
{
int loadPercent = 100;
if (!cached)
{
// Building the cache will take 95% of the load time.
loadPercent = 5;
status = status.ChangeMessage(string.Format(Resources.XHunterLibrary_Load_Building_binary_cache_for__0__library, Path.GetFileName(FilePath)));
status = status.ChangePercentComplete(0);
loader.UpdateProgress(status);
if (!CreateCache(loader, status, 100 - loadPercent))
{
return(false);
}
}
status = status.ChangeMessage(string.Format(Resources.XHunterLibrary_Load_Loading__0__library, Path.GetFileName(FilePath)));
loader.UpdateProgress(status);
var sm = loader.StreamManager;
using (Stream stream = sm.CreateStream(CachePath, FileMode.Open, true))
{
// Read library header from the end of the cache
int countHeader = (int)LibHeaders.count * sizeof(int);
stream.Seek(-countHeader, SeekOrigin.End);
byte[] libHeader = new byte[countHeader];
ReadComplete(stream, libHeader, countHeader);
int version = GetInt32(libHeader, (int)LibHeaders.format_version);
if (version != FORMAT_VERSION_CACHE)
{
return(false);
}
int countRevisionBytes = GetInt32(libHeader, (int)LibHeaders.revision_byte_count);
int countIdBytes = GetInt32(libHeader, (int)LibHeaders.id_byte_count);
stream.Seek(-countHeader - countRevisionBytes - countIdBytes, SeekOrigin.End);
Revision = ReadString(stream, countRevisionBytes);
Id = ReadString(stream, countIdBytes);
int numSpectra = GetInt32(libHeader, (int)LibHeaders.num_spectra);
var setSequences = new Dictionary <LibSeqKey, bool>(numSpectra);
var libraryEntries = new XHunterSpectrumInfo[numSpectra];
// Seek to beginning of spectrum headers
long locationHeaders = BitConverter.ToInt64(libHeader,
((int)LibHeaders.location_headers_lo) * sizeof(int));
stream.Seek(locationHeaders, SeekOrigin.Begin);
byte[] specSequence = new byte[1024];
byte[] specHeader = new byte[1024];
countHeader = (int)SpectrumCacheHeader.count * 4;
for (int i = 0; i < numSpectra; i++)
{
int percent = (100 - loadPercent) + (i * loadPercent / numSpectra);
if (status.PercentComplete != percent)
{
// Check for cancellation after each integer change in percent loaded.
if (loader.IsCanceled)
{
loader.UpdateProgress(status.Cancel());
return(false);
}
// If not cancelled, update progress.
loader.UpdateProgress(status = status.ChangePercentComplete(percent));
}
// Read spectrum header
ReadComplete(stream, specHeader, countHeader);
int seqKeyHash = GetInt32(specHeader, ((int)SpectrumCacheHeader.seq_key_hash));
int seqKeyLength = GetInt32(specHeader, ((int)SpectrumCacheHeader.seq_key_length));
int charge = GetInt32(specHeader, ((int)SpectrumCacheHeader.charge));
if (charge == 0 || charge > TransitionGroup.MAX_PRECURSOR_CHARGE)
{
throw new InvalidDataException(Resources.XHunterLibrary_Load_Invalid_precursor_charge_found_File_may_be_corrupted);
}
float i2 = BitConverter.ToSingle(specHeader, ((int)SpectrumCacheHeader.i2) * 4);
long location = BitConverter.ToInt64(specHeader, ((int)SpectrumCacheHeader.location_lo) * 4);
int numPeaks = GetInt32(specHeader, ((int)SpectrumCacheHeader.num_peaks));
float expect = BitConverter.ToSingle(specHeader, ((int)SpectrumCacheHeader.expect) * 4);
int seqLength = GetInt32(specHeader, (int)SpectrumCacheHeader.seq_len);
// Read sequence information
ReadComplete(stream, specSequence, seqLength);
LibKey key = new LibKey(specSequence, 0, seqLength, charge);
libraryEntries[i] = new XHunterSpectrumInfo(key, i2, expect, (short)numPeaks, location);
if (seqKeyLength > 0)
{
LibSeqKey seqKey = new LibSeqKey(key, seqKeyHash, seqKeyLength);
setSequences.Add(seqKey, true);
}
}
// Checksum = checksum.ChecksumValue;
_libraryEntries = libraryEntries;
_setSequences = setSequences;
loader.UpdateProgress(status.Complete());
// Create the stream from which the spectra will be read
CreateStream(loader);
}
return(true);
}
catch (InvalidDataException x)
{
if (!cached)
{
loader.UpdateProgress(status.ChangeErrorException(x));
}
return(false);
}
catch (IOException x)
{
if (!cached)
{
loader.UpdateProgress(status.ChangeErrorException(x));
}
return(false);
}
catch (Exception x)
{
if (!cached)
{
x = new Exception(string.Format(Resources.XHunterLibrary_Load_Failed_loading_library__0__, FilePath), x);
loader.UpdateProgress(status.ChangeErrorException(x));
}
return(false);
}
finally
{
if (ReadStream != null)
{
// Close the read stream to ensure we never leak it.
// This only costs on extra open, the first time the
// active document tries to read.
try { ReadStream.CloseStream(); }
catch (IOException) { }
}
}
}
// ReSharper restore LocalizableElement
public static List <string> ConvertPilotFiles(IList <string> inputFiles, IProgressMonitor progress, IProgressStatus status)
{
string groupConverterExePath = null;
var inputFilesPilotConverted = new List <string>();
for (int index = 0; index < inputFiles.Count; index++)
{
string inputFile = inputFiles[index];
if (!inputFile.EndsWith(BiblioSpecLiteBuilder.EXT_PILOT))
{
inputFilesPilotConverted.Add(inputFile);
continue;
}
string outputFile = Path.ChangeExtension(inputFile, BiblioSpecLiteBuilder.EXT_PILOT_XML);
// Avoid re-converting files that have already been converted
if (File.Exists(outputFile))
{
// Avoid duplication, in case the user accidentally adds both .group and .group.xml files
// for the same results
if (!inputFiles.Contains(outputFile))
{
inputFilesPilotConverted.Add(outputFile);
}
continue;
}
string message = string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Converting__0__to_xml, Path.GetFileName(inputFile));
int percent = index * 100 / inputFiles.Count;
progress.UpdateProgress(status = status.ChangeMessage(message).ChangePercentComplete(percent));
if (groupConverterExePath == null)
{
var key = Registry.LocalMachine.OpenSubKey(KEY_PROTEIN_PILOT, false);
if (key != null)
{
string proteinPilotCommandWithArgs = (string)key.GetValue(string.Empty);
var proteinPilotCommandWithArgsSplit =
// ReSharper disable LocalizableElement
proteinPilotCommandWithArgs.Split(new[] { "\" \"" }, StringSplitOptions.RemoveEmptyEntries); // Remove " "%1"
// ReSharper restore LocalizableElement
string path = Path.GetDirectoryName(proteinPilotCommandWithArgsSplit[0].Trim(new[] { '\\', '\"' })); // Remove preceding "
if (!string.IsNullOrEmpty(path))
{
var groupFileExtractorPath = Path.Combine(path, EXE_GROUP_FILE_EXTRACTOR);
if (File.Exists(groupFileExtractorPath))
{
groupConverterExePath = groupFileExtractorPath;
}
else
{
var group2XmlPath = Path.Combine(path, EXE_GROUP2_XML);
if (File.Exists(group2XmlPath))
{
groupConverterExePath = group2XmlPath;
}
else
{
string errorMessage = string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Unable_to_find__0__or__1__in_directory__2____Please_reinstall_ProteinPilot_software_to_be_able_to_handle__group_files_,
EXE_GROUP_FILE_EXTRACTOR, EXE_GROUP2_XML, path);
throw new IOException(errorMessage);
}
}
}
}
if (groupConverterExePath == null)
{
throw new IOException(Resources.VendorIssueHelper_ConvertPilotFiles_ProteinPilot_software__trial_or_full_version__must_be_installed_to_convert___group__files_to_compatible___group_xml__files_);
}
}
// run group2xml
// ReSharper disable LocalizableElement
var argv = new[]
{
"XML",
"\"" + inputFile + "\"",
"\"" + outputFile + "\""
};
// ReSharper restore LocalizableElement
var psi = new ProcessStartInfo(groupConverterExePath)
{
CreateNoWindow = true,
UseShellExecute = false,
// Common directory includes the directory separator
// ReSharper disable once ConstantNullCoalescingCondition
WorkingDirectory = Path.GetDirectoryName(groupConverterExePath) ?? string.Empty,
Arguments = string.Join(@" ", argv.ToArray()),
RedirectStandardError = true,
RedirectStandardOutput = true,
};
var sbOut = new StringBuilder();
var proc = new Process {
StartInfo = psi
};
proc.Start();
var reader = new ProcessStreamReader(proc);
string line;
while ((line = reader.ReadLine()) != null)
{
if (progress.IsCanceled)
{
proc.Kill();
throw new LoadCanceledException(status.Cancel());
}
sbOut.AppendLine(line);
}
while (!proc.WaitForExit(200))
{
if (progress.IsCanceled)
{
proc.Kill();
return(inputFilesPilotConverted);
}
}
if (proc.ExitCode != 0)
{
throw new IOException(TextUtil.LineSeparate(string.Format(Resources.VendorIssueHelper_ConvertPilotFiles_Failure_attempting_to_convert_file__0__to__group_xml_,
inputFile), string.Empty, sbOut.ToString()));
}
inputFilesPilotConverted.Add(outputFile);
}
progress.UpdateProgress(status.ChangePercentComplete(100));
return(inputFilesPilotConverted);
}
