protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
// Only allow one background proteome to load at a time. This can
// get tricky, if the user performs an undo and then a redo across
// a change in background proteome.
// Our first priority is doing the digestions, the second is accessing web
// services to add missing protein metadata.
lock (_lockLoadBackgroundProteome)
{
BackgroundProteome originalBackgroundProteome = GetBackgroundProteome(docCurrent);
// Check to see whether the Digestion already exists but has not been queried yet.
BackgroundProteome backgroundProteomeWithDigestions = new BackgroundProteome(originalBackgroundProteome, true);
if (IsNotLoadedExplained(docCurrent, backgroundProteomeWithDigestions, true) == null)
{
// digest is ready, and protein metdata is resolved
CompleteProcessing(container, backgroundProteomeWithDigestions);
return(true);
}
// are we here to do the digest, or to resolve the protein metadata?
bool getMetadata = (IsNotLoadedExplained(docCurrent, backgroundProteomeWithDigestions, false) == null) &&
backgroundProteomeWithDigestions.NeedsProteinMetadataSearch;
string name = originalBackgroundProteome.Name;
ProgressStatus progressStatus =
new ProgressStatus(string.Format(getMetadata?Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome:Resources.BackgroundProteomeManager_LoadBackground_Digesting__0__proteome, name));
try
{
using (FileSaver fs = new FileSaver(originalBackgroundProteome.DatabasePath, StreamManager))
{
File.Copy(originalBackgroundProteome.DatabasePath, fs.SafeName, true);
var digestHelper = new DigestHelper(this, container, docCurrent, name, fs.SafeName, true);
bool success;
if (getMetadata)
{
success = digestHelper.LookupProteinMetadata(ref progressStatus);
}
else
{
success = (digestHelper.Digest(ref progressStatus) != null);
}
if (!success)
{
// Processing was canceled
EndProcessing(docCurrent);
UpdateProgress(progressStatus.Cancel());
return(false);
}
using (var proteomeDb = ProteomeDb.OpenProteomeDb(originalBackgroundProteome.DatabasePath))
{
proteomeDb.DatabaseLock.AcquireWriterLock(int.MaxValue);
try
{
if (!fs.Commit())
{
EndProcessing(docCurrent);
throw new IOException(
string.Format(
Resources
.BackgroundProteomeManager_LoadBackground_Unable_to_rename_temporary_file_to__0__,
fs.RealName));
}
}
finally
{
proteomeDb.DatabaseLock.ReleaseWriterLock();
}
}
CompleteProcessing(container, new BackgroundProteome(originalBackgroundProteome, true));
UpdateProgress(progressStatus.Complete());
return(true);
}
}
catch (Exception x)
{
var message = new StringBuilder();
message.AppendLine(
string.Format(Resources.BackgroundProteomeManager_LoadBackground_Failed_updating_background_proteome__0__,
name));
message.Append(x.Message);
UpdateProgress(progressStatus.ChangeErrorException(new IOException(message.ToString(), x)));
return(false);
}
}
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
// Only allow one background proteome to load at a time. This can
// get tricky, if the user performs an undo and then a redo across
// a change in background proteome.
// Our first priority is doing the digestions, the second is accessing web
// services to add missing protein metadata.
lock (_lockLoadBackgroundProteome)
{
BackgroundProteome originalBackgroundProteome = GetBackgroundProteome(docCurrent);
// Check to see whether the Digestion already exists but has not been queried yet.
BackgroundProteome backgroundProteomeWithDigestions = new BackgroundProteome(originalBackgroundProteome, true);
if (IsNotLoadedExplained(docCurrent, backgroundProteomeWithDigestions, true) == null)
{
// digest is ready, and protein metdata is resolved
CompleteProcessing(container, backgroundProteomeWithDigestions);
return true;
}
// are we here to do the digest, or to resolve the protein metadata?
bool getMetadata = (IsNotLoadedExplained(docCurrent, backgroundProteomeWithDigestions, false) == null) &&
backgroundProteomeWithDigestions.NeedsProteinMetadataSearch;
string name = originalBackgroundProteome.Name;
ProgressStatus progressStatus =
new ProgressStatus(string.Format(getMetadata?Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome:Resources.BackgroundProteomeManager_LoadBackground_Digesting__0__proteome, name));
try
{
using (FileSaver fs = new FileSaver(originalBackgroundProteome.DatabasePath, StreamManager))
{
File.Copy(originalBackgroundProteome.DatabasePath, fs.SafeName, true);
var digestHelper = new DigestHelper(this, container, docCurrent, name, fs.SafeName, true);
bool success;
if (getMetadata)
success = digestHelper.LookupProteinMetadata(ref progressStatus);
else
success = (digestHelper.Digest(ref progressStatus) != null);
if (!success)
{
// Processing was canceled
EndProcessing(docCurrent);
UpdateProgress(progressStatus.Cancel());
return false;
}
using (var proteomeDb = ProteomeDb.OpenProteomeDb(originalBackgroundProteome.DatabasePath))
{
proteomeDb.DatabaseLock.AcquireWriterLock(int.MaxValue);
try
{
if (!fs.Commit())
{
EndProcessing(docCurrent);
throw new IOException(
string.Format(
Resources
.BackgroundProteomeManager_LoadBackground_Unable_to_rename_temporary_file_to__0__,
fs.RealName));
}
}
finally
{
proteomeDb.DatabaseLock.ReleaseWriterLock();
}
}
CompleteProcessing(container, new BackgroundProteome(originalBackgroundProteome, true));
UpdateProgress(progressStatus.Complete());
return true;
}
}
catch (Exception x)
{
var message = new StringBuilder();
message.AppendLine(
string.Format(Resources.BackgroundProteomeManager_LoadBackground_Failed_updating_background_proteome__0__,
name));
message.Append(x.Message);
UpdateProgress(progressStatus.ChangeErrorException(new IOException(message.ToString(), x)));
return false;
}
}
}
private BackgroundProteome Load(IDocumentContainer container, PeptideSettings settings, SrmDocument docCurrent, bool isBackgroundLoad)
{
// Only allow one background proteome to load at a time. This can
// get tricky, if the user performs an undo and then a redo across
// a change in background proteome.
// Our first priority is doing the digestions, the second is accessing web
// services to add missing protein metadata.
// There may also be a load initiation by the Peptide Settings dialog as foreground task,
// it takes priority over the background task.
lock (_lockLoadBackgroundProteome)
{
BackgroundProteome originalBackgroundProteome = settings.BackgroundProteome;
// Check to see whether the Digestion already exists but has not been queried yet.
BackgroundProteome backgroundProteomeWithDigestions = new BackgroundProteome(originalBackgroundProteome, true);
if (IsNotLoadedExplained(settings, backgroundProteomeWithDigestions, true) == null)
{
// digest is ready, and protein metdata is resolved
CompleteProcessing(container, backgroundProteomeWithDigestions);
return(originalBackgroundProteome); // No change needed
}
// are we here to do the digest, or to resolve the protein metadata?
var needsProteinMetadataSearch = backgroundProteomeWithDigestions.NeedsProteinMetadataSearch;
bool getMetadata = (IsNotLoadedExplained(settings, backgroundProteomeWithDigestions, false) == null) &&
needsProteinMetadataSearch;
string name = originalBackgroundProteome.Name;
IProgressStatus progressStatus =
new ProgressStatus(string.Format(getMetadata?Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome:Resources.BackgroundProteomeManager_LoadBackground_Digesting__0__proteome, name));
try
{
// The transaction commit for writing the digestion info can be very lengthy, avoid lock timeouts
// by doing that work in a tempfile that no other thread knows aboout
using (FileSaver fs = new FileSaver(originalBackgroundProteome.DatabasePath, StreamManager))
{
File.Copy(originalBackgroundProteome.DatabasePath, fs.SafeName, true);
var digestHelper = new DigestHelper(this, container, docCurrent, settings, name, fs.SafeName, true);
bool success;
if (getMetadata)
{
success = digestHelper.LookupProteinMetadata(ref progressStatus);
}
else
{
success = digestHelper.Digest(ref progressStatus, true); // Delay indexing until we copy the file back
}
if (digestHelper.IsCanceled || !success)
{
// Processing was canceled
if (docCurrent != null)
{
EndProcessing(docCurrent);
}
UpdateProgress(progressStatus.Cancel());
return(null);
}
using (var proteomeDb = ProteomeDb.OpenProteomeDb(originalBackgroundProteome.DatabasePath))
{
proteomeDb.DatabaseLock.AcquireWriterLock(int.MaxValue); // Wait for any existing readers to complete, prevent any new ones
try
{
if (File.GetLastWriteTime(fs.RealName) <= File.GetLastWriteTime(fs.SafeName)) // Don't overwrite if foreground task has already updated
{
proteomeDb.CloseDbConnection(); // Get rid of any file handles
if (!fs.Commit())
{
if (docCurrent != null)
{
EndProcessing(docCurrent);
}
throw new IOException(string.Format(Resources.BackgroundProteomeManager_LoadBackground_Unable_to_rename_temporary_file_to__0__,
fs.RealName));
}
}
}
finally
{
proteomeDb.DatabaseLock.ReleaseWriterLock();
}
}
var proteomeWithDigestions = new BackgroundProteome(originalBackgroundProteome, true);
using (var proteomeDb = proteomeWithDigestions.OpenProteomeDb())
{
proteomeDb.AnalyzeDb(); // Now it's safe to start this potentially lengthy indexing operation
}
CompleteProcessing(container, proteomeWithDigestions);
UpdateProgress(progressStatus.Complete());
return(proteomeWithDigestions);
}
}
catch (Exception x)
{
var message = new StringBuilder();
message.AppendLine(
string.Format(Resources.BackgroundProteomeManager_LoadBackground_Failed_updating_background_proteome__0__,
name));
message.Append(x.Message);
UpdateProgress(progressStatus.ChangeErrorException(new IOException(message.ToString(), x)));
return(null);
}
}
}