public void ProteinListTest()
{
// Too few columns
const char sep = TextUtil.SEPARATOR_TSV;
AssertEx.ThrowsException <LineColNumberedIoException>(() =>
FastaImporter.ToFasta("PROT1\nPROT2\nPROT2", sep));
// Invalid sequence
string invalidSeq = PROTEINLIST_CLIPBOARD_TEXT.Replace("MDAL", "***");
AssertEx.ThrowsException <LineColNumberedIoException>(() =>
FastaImporter.ToFasta(invalidSeq, sep));
string fastaText = FastaImporter.ToFasta(PROTEINLIST_CLIPBOARD_TEXT, sep);
var reader = new StringReader(fastaText);
int countProt = 0;
string line;
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith(">"))
{
countProt++;
}
else
{
Assert.IsTrue(FastaSequence.IsExSequence(line.Trim('*')));
}
}
Assert.AreEqual(3, countProt);
}
public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out List <PeptideGroupDocNode> peptideGroupsNew)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
peptideGroupsNew = importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)).ToList();
document = document.AddPeptideGroups(peptideGroupsNew, false, to, out firstAdded, out nextAdd);
}
return(document);
}
public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out int emptyProteinCount)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
document = document.AddPeptideGroups(importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)),
false, null, out firstAdded, out nextAdd);
}
emptyProteinCount = importer.EmptyPeptideGroupCount;
return(document);
}
public static OptimizationDb ConvertFromOldFormat(string path, IProgressMonitor loadMonitor, ProgressStatus status, SrmDocument document)
{
// Try to open assuming old format (Id, PeptideModSeq, Charge, Mz, Value, Type)
var precursors = new Dictionary<string, HashSet<int>>(); // PeptideModSeq -> charges
var optimizations = new List<Tuple<DbOptimization, double>>(); // DbOptimization, product m/z
int maxCharge = 1;
using (SQLiteConnection connection = new SQLiteConnection("Data Source = " + path)) // Not L10N
using (SQLiteCommand command = new SQLiteCommand(connection))
{
connection.Open();
command.CommandText = "SELECT PeptideModSeq, Charge, Mz, Value, Type FROM OptimizationLibrary"; // Not L10N
using (SQLiteDataReader reader = command.ExecuteReader())
{
while (reader.Read())
{
var type = (OptimizationType)reader["Type"]; // Not L10N
var modifiedSequence = reader["PeptideModSeq"].ToString(); // Not L10N
var charge = (int)reader["Charge"]; // Not L10N
var productMz = (double)reader["Mz"]; // Not L10N
var value = (double)reader["Value"]; // Not L10N
optimizations.Add(new Tuple<DbOptimization, double>(new DbOptimization(type, modifiedSequence, charge, string.Empty, -1, value), productMz));
if (!precursors.ContainsKey(modifiedSequence))
{
precursors[modifiedSequence] = new HashSet<int>();
}
precursors[modifiedSequence].Add(charge);
if (charge > maxCharge)
{
maxCharge = charge;
}
}
}
}
var peptideList = (from precursor in precursors
from charge in precursor.Value
select string.Format("{0}{1}", precursor.Key, Transition.GetChargeIndicator(charge)) // Not L10N
).ToList();
var newDoc = new SrmDocument(document != null ? document.Settings : SrmSettingsList.GetDefault());
newDoc = newDoc.ChangeSettings(newDoc.Settings
.ChangePeptideLibraries(libs => libs.ChangePick(PeptidePick.filter))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName("ion 1") // Not L10N
.ChangeFragmentRangeLastName("last ion") // Not L10N
.ChangeProductCharges(Enumerable.Range(1, maxCharge).ToList())
.ChangeIonTypes(new []{ IonType.y, IonType.b }))
.ChangeTransitionLibraries(libs => libs.ChangePick(TransitionLibraryPick.none))
);
var matcher = new ModificationMatcher { FormatProvider = NumberFormatInfo.InvariantInfo };
matcher.CreateMatches(newDoc.Settings, peptideList, Settings.Default.StaticModList, Settings.Default.HeavyModList);
FastaImporter importer = new FastaImporter(newDoc, matcher);
string text = string.Format(">>{0}\r\n{1}", newDoc.GetPeptideGroupId(true), TextUtil.LineSeparate(peptideList)); // Not L10N
PeptideGroupDocNode imported = importer.Import(new StringReader(text), null, Helpers.CountLinesInString(text)).First();
int optimizationsUpdated = 0;
foreach (PeptideDocNode nodePep in imported.Children)
{
string sequence = newDoc.Settings.GetSourceTextId(nodePep);
foreach (var nodeGroup in nodePep.TransitionGroups)
{
int charge = nodeGroup.PrecursorCharge;
foreach (var nodeTran in nodeGroup.Transitions)
{
double productMz = nodeTran.Mz;
foreach (var optimization in optimizations.Where(opt =>
string.IsNullOrEmpty(opt.Item1.FragmentIon) &&
opt.Item1.ProductCharge == -1 &&
opt.Item1.PeptideModSeq == sequence &&
opt.Item1.Charge == charge &&
Math.Abs(opt.Item2 - productMz) < 0.00001))
{
optimization.Item1.FragmentIon = nodeTran.FragmentIonName;
optimization.Item1.ProductCharge = nodeTran.Transition.Charge;
++optimizationsUpdated;
}
}
}
}
if (optimizations.Count > optimizationsUpdated)
{
throw new OptimizationsOpeningException(string.Format(Resources.OptimizationDb_ConvertFromOldFormat_Failed_to_convert__0__optimizations_to_new_format_,
optimizations.Count - optimizationsUpdated));
}
using (var fs = new FileSaver(path))
{
OptimizationDb db = CreateOptimizationDb(fs.SafeName);
db.UpdateOptimizations(optimizations.Select(opt => opt.Item1).ToArray(), new DbOptimization[0]);
fs.Commit();
if (loadMonitor != null)
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
return GetOptimizationDb(fs.RealName, null, null);
}
}
public static OptimizationDb ConvertFromOldFormat(string path, IProgressMonitor loadMonitor, ProgressStatus status, SrmDocument document)
{
// Try to open assuming old format (Id, PeptideModSeq, Charge, Mz, Value, Type)
var precursors = new Dictionary <Target, HashSet <int> >(); // PeptideModSeq -> charges
var optimizations = new List <Tuple <DbOptimization, double> >(); // DbOptimization, product m/z
int maxCharge = 1;
using (SQLiteConnection connection = new SQLiteConnection(@"Data Source = " + path))
using (SQLiteCommand command = new SQLiteCommand(connection))
{
connection.Open();
command.CommandText = @"SELECT PeptideModSeq, Charge, Mz, Value, Type FROM OptimizationLibrary";
using (SQLiteDataReader reader = command.ExecuteReader())
{
while (reader.Read())
{
var type = (OptimizationType)reader[@"Type"];
var modifiedSequence = new Target(reader[@"PeptideModSeq"].ToString());
var charge = (int)reader[@"Charge"];
var productMz = (double)reader[@"Mz"];
var value = (double)reader[@"Value"];
optimizations.Add(new Tuple <DbOptimization, double>(new DbOptimization(type, modifiedSequence, Adduct.FromChargeProtonated(charge), string.Empty, Adduct.EMPTY, value), productMz));
if (!precursors.ContainsKey(modifiedSequence))
{
precursors[modifiedSequence] = new HashSet <int>();
}
precursors[modifiedSequence].Add(charge);
if (charge > maxCharge)
{
maxCharge = charge;
}
}
}
}
var peptideList = (from precursor in precursors
from charge in precursor.Value
select string.Format(@"{0}{1}", precursor.Key, Transition.GetChargeIndicator(Adduct.FromChargeProtonated(charge)))
).ToList();
var newDoc = new SrmDocument(document != null ? document.Settings : SrmSettingsList.GetDefault());
newDoc = newDoc.ChangeSettings(newDoc.Settings
.ChangePeptideLibraries(libs => libs.ChangePick(PeptidePick.filter))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName(@"ion 1")
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideProductCharges(Enumerable.Range(1, maxCharge).Select(Adduct.FromChargeProtonated).ToList()) // TODO(bspratt) negative charge peptides
.ChangePeptideIonTypes(new [] { IonType.y, IonType.b })) // TODO(bspratt) generalize to molecules?
.ChangeTransitionLibraries(libs => libs.ChangePick(TransitionLibraryPick.none))
);
var matcher = new ModificationMatcher();
matcher.CreateMatches(newDoc.Settings, peptideList, Settings.Default.StaticModList, Settings.Default.HeavyModList);
FastaImporter importer = new FastaImporter(newDoc, matcher);
// ReSharper disable LocalizableElement
string text = string.Format(">>{0}\r\n{1}", newDoc.GetPeptideGroupId(true), TextUtil.LineSeparate(peptideList));
// ReSharper restore LocalizableElement
PeptideGroupDocNode imported = importer.Import(new StringReader(text), null, Helpers.CountLinesInString(text)).First();
int optimizationsUpdated = 0;
foreach (PeptideDocNode nodePep in imported.Children)
{
foreach (var nodeGroup in nodePep.TransitionGroups)
{
var charge = nodeGroup.PrecursorAdduct;
var libKeyToMatch = newDoc.Settings.GetSourceTarget(nodePep).GetLibKey(charge).LibraryKey;
foreach (var nodeTran in nodeGroup.Transitions)
{
double productMz = nodeTran.Mz;
foreach (var optimization in optimizations.Where(opt =>
string.IsNullOrEmpty(opt.Item1.FragmentIon) &&
opt.Item1.ProductAdduct.IsEmpty &&
Math.Abs(opt.Item2 - productMz) < 0.00001))
{
var optLibKey = optimization.Item1.Target.GetLibKey(optimization.Item1.Adduct).LibraryKey;
if (!LibKeyIndex.KeysMatch(optLibKey, libKeyToMatch))
{
continue;
}
optimization.Item1.FragmentIon = nodeTran.FragmentIonName;
optimization.Item1.ProductAdduct = nodeTran.Transition.Adduct;
++optimizationsUpdated;
}
}
}
}
if (optimizations.Count > optimizationsUpdated)
{
throw new OptimizationsOpeningException(string.Format(Resources.OptimizationDb_ConvertFromOldFormat_Failed_to_convert__0__optimizations_to_new_format_,
optimizations.Count - optimizationsUpdated));
}
using (var fs = new FileSaver(path))
{
OptimizationDb db = CreateOptimizationDb(fs.SafeName);
db.UpdateOptimizations(optimizations.Select(opt => opt.Item1).ToArray(), new DbOptimization[0]);
fs.Commit();
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
return(GetOptimizationDb(fs.RealName, null, null));
}
}
protected override void DoTest()
{
OpenDocument("Rat_plasma.sky");
RunUI(SkylineWindow.ShowAuditLog);
var auditLogForm = WaitForOpenForm <AuditLogForm>();
Assert.IsFalse(SkylineWindow.Document.Settings.DataSettings.AuditLogging);
RunUI(() => auditLogForm.EnableAuditLogging(true));
// Test that initial hash is correct
var expectedHash = BlockHash.SafeToBase64(new byte[]
{
0xFE, 0x0F, 0x0C, 0x54,
0xA0, 0x77, 0xE5, 0x8F,
0x77, 0xDC, 0x8B, 0xEE,
0x44, 0xB6, 0x65, 0x6D,
0x98, 0x31, 0xAA, 0x35
});
var actualHash = GetDocumentHash();
Assert.AreEqual(expectedHash, actualHash);
// Test that the hash is the same as if the document was simply read and hashed
// The document is really small (<20KB) so it's fine to read it all into memory
var bytes = File.ReadAllBytes(SkylineWindow.DocumentFilePath);
var hash = Hash(bytes);
Assert.AreEqual(expectedHash, hash);
// Make sure that there's an entry describing 1) number of nodes and 2) settings changes from default settings
Assert.AreEqual(1, SkylineWindow.Document.AuditLog.AuditLogEntries.Count);
if (!RecordNewestEntry())
{
RunUI(() => { LOG_ENTRY_MESSAGES[0].AssertEquals(SkylineWindow.Document.AuditLog.AuditLogEntries); });
}
// Modify and save the document so that the audit log gets saved
ChangeSettings(settings => settings.ChangePeptideFilter(filter => filter.ChangeExcludeNTermAAs(3))); // Change from 2 to 3
RunUI(() => SkylineWindow.SaveDocument());
RecordNewestEntry();
Assert.IsTrue(File.Exists(SrmDocument.GetAuditLogPath(SkylineWindow.DocumentFilePath)), "Audit log does not exist after saving document");
AssertEx.ValidateAuditLogAgainstSchema(File.ReadAllText(SrmDocument.GetAuditLogPath(SkylineWindow.DocumentFilePath)));
// Also validate an old document
AssertEx.ValidateAuditLogAgainstSchema(File.ReadAllText(TestFilesDir.GetTestPath("old_rat_plasma.skyl")));
// Modify document outside of skyline
var docPath = SkylineWindow.DocumentFilePath;
RunUI(() => SkylineWindow.NewDocument(true));
// Audit logging should be enabled since the previous settings will be used
Assert.IsTrue(SkylineWindow.Document.Settings.DataSettings.AuditLogging);
// Perform the following action manually:
// Settings > Peptide Settings -- Filter > Exclude N-Terminal AA's changed from "3" to "4"
var text = File.ReadAllText(docPath);
var match = Regex.Match(text, "<peptide_filter .*start=\"3\"");
Assert.IsTrue(match.Success);
Assert.IsFalse(match.NextMatch().Success);
var sb = new StringBuilder(text);
sb[match.Index + match.Length - 2] = '4';
File.WriteAllText(docPath, sb.ToString());
var oldRef = SkylineWindow.Document;
// Add an entry describing this change
OpenDocumentNoWait("Rat_plasma.sky");
var alert = WaitForOpenForm <AlertDlg>();
OkDialog(alert, alert.ClickYes);
var logForm = WaitForOpenForm <DocumentChangeLogEntryDlg>();
RunUI(() => { logForm.LogMessage = "Changed Exlude N-Terminal AA's from 3 to 4 manually"; });
OkDialog(logForm, logForm.OkDialog);
// Wait until document gets switched, otherwise WaitForDocumentLoaded will think that the document is already loaded
// since we're not waiting for the document to open (OpenDocumentNoWait)
WaitForCondition(() => !ReferenceEquals(oldRef, SkylineWindow.Document));
Assert.AreNotEqual(expectedHash, SkylineWindow.Document.DocumentHash); // If this wasn't the case the dialogs would never show up, but check anyways
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SaveDocument()); // Save so that hash in audit log matches document now
// Now audit logging should be enabled
Assert.IsTrue(SkylineWindow.Document.Settings.DataSettings.AuditLogging);
// Make sure the entry was actually added
Assert.AreEqual(3, SkylineWindow.Document.AuditLog.AuditLogEntries.Count);
// Check that this entry got saved and read correctly, we don't record here
if (!IsRecordMode)
{
RunUI(() => { LOG_ENTRY_MESSAGES[1].AssertEquals(SkylineWindow.Document.AuditLog.AuditLogEntries.Parent); });
}
if (!RecordNewestEntry())
{
RunUI(() => { LOG_ENTRY_MESSAGES[2].AssertEquals(SkylineWindow.Document.AuditLog.AuditLogEntries); });
}
var fasta = FastaImporter.ToFasta(PROTEINLIST_CLIPBOARD_TEXT, TextUtil.SEPARATOR_TSV);
RunDlg <EmptyProteinsDlg>(() => SkylineWindow.Paste(fasta), dlg => dlg.KeepEmptyProteins());
if (!RecordNewestEntry())
{
RunUI(() => { LOG_ENTRY_MESSAGES[3].AssertEquals(SkylineWindow.Document.AuditLog.AuditLogEntries); });
}
RunUI(SkylineWindow.ShowAuditLog);
var auditLogForm1 = WaitForOpenForm <AuditLogForm>();
RunUI(() => auditLogForm1.ChooseView(AuditLogStrings.AuditLogForm_MakeAuditLogForm_Undo_Redo));
AuditLogUtil.WaitForAuditLogForm(auditLogForm1);
// Show extra info for this entry
RunDlg <AuditLogExtraInfoForm>(() =>
{
Assert.AreEqual(4, auditLogForm1.DataGridView.RowCount);
var fastaRow = auditLogForm1.DataGridView.Rows[0];
var undoRedoCol = auditLogForm1.FindColumn(nameof(AuditLogRow.UndoRedoMessage));
Assert.IsNotNull(undoRedoCol);
var auditLogRowText = fastaRow.Cells[undoRedoCol.Index].Value as AuditLogRow.AuditLogRowText;
Assert.IsNotNull(auditLogRowText);
var col = auditLogForm1.DataGridView.Columns[undoRedoCol.Index] as AuditLogColumn;
Assert.IsNotNull(col);
Assert.IsTrue(col.ShouldDisplay(auditLogRowText, (int)AuditLogColumn.ImageIndex.extra_info));
col.Click(auditLogRowText, (int)AuditLogColumn.ImageIndex.extra_info);
}, form =>
{
var entry = SkylineWindow.DocumentUI.AuditLog.AuditLogEntries;
Assert.AreEqual(form.Message, entry.UndoRedo.ToString());
Assert.AreEqual(form.ExtraInfo, entry.ExtraInfo);
form.OkDialog();
});
// Disable audit logging, this should warn the user
RunDlg <AlertDlg>(() => { auditLogForm1.EnableAuditLogging(false); }, alertDlg => { alertDlg.ClickYes(); });
AuditLogUtil.WaitForAuditLogForm(auditLogForm1);
Assert.AreEqual(0, SkylineWindow.Document.AuditLog.AuditLogEntries.Count);
Assert.IsFalse(SkylineWindow.Document.Settings.DataSettings.AuditLogging);
// Re-open document without saving
RunUI(() => SkylineWindow.NewDocument(true));
OpenDocument("Rat_plasma.sky");
RunUI(SkylineWindow.ShowAuditLog);
var auditLogForm2 = WaitForOpenForm <AuditLogForm>();
RunUI(() => auditLogForm2.ChooseView(AuditLogStrings.AuditLogForm_MakeAuditLogForm_Undo_Redo));
AuditLogUtil.WaitForAuditLogForm(auditLogForm2);
RunUI(() =>
{
// Audit logging shold be back on and the entries should still be there
Assert.IsTrue(SkylineWindow.DocumentUI.Settings.DataSettings.AuditLogging);
Assert.AreEqual(3, SkylineWindow.DocumentUI.AuditLog.AuditLogEntries.Count);
});
// Disable again, this time save
RunDlg <AlertDlg>(() => { auditLogForm2.EnableAuditLogging(false); }, alertDlg => { alertDlg.ClickYes(); });
RunUI(() => SkylineWindow.SaveDocument());
// audit log should be gone
Assert.IsFalse(File.Exists(SrmDocument.GetAuditLogPath(SkylineWindow.DocumentFilePath)));
}
