public RemoteChromDataProvider(SrmDocument document, IRetentionTimePredictor retentionTimePredictor, ChromFileInfo chromFileInfo, IProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
_document = document;
ChorusUrl chorusUrl = (ChorusUrl)chromFileInfo.FilePath;
_chorusAccount = chorusUrl.FindChorusAccount(Settings.Default.RemoteAccountList);
var chromatogramRequestProviders = new List <ChromatogramRequestProvider>();
foreach (bool firstPass in new[] { true, false })
{
if (null == retentionTimePredictor && !firstPass)
{
continue;
}
var chromatogramRequestProvider = new ChromatogramRequestProvider(document, chorusUrl,
retentionTimePredictor, firstPass);
if (0 == chromatogramRequestProvider.ChromKeys.Count)
{
continue;
}
chromatogramRequestProviders.Add(chromatogramRequestProvider);
}
_chromatogramRequestProviders = chromatogramRequestProviders.ToArray();
_chromTaskLists = new ChromTaskList[_chromatogramRequestProviders.Length];
}
public RemoteChromDataProvider(SrmDocument document, IRetentionTimePredictor retentionTimePredictor, ChromFileInfo chromFileInfo, ProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
_document = document;
ChorusUrl chorusUrl = (ChorusUrl)chromFileInfo.FilePath;
_chorusAccount = chorusUrl.FindChorusAccount(Settings.Default.ChorusAccountList);
var chromatogramRequestProviders = new List<ChromatogramRequestProvider>();
foreach (bool firstPass in new[] {true, false})
{
if (null == retentionTimePredictor && !firstPass)
{
continue;
}
var chromatogramRequestProvider = new ChromatogramRequestProvider(document, chorusUrl,
retentionTimePredictor, firstPass);
if (0 == chromatogramRequestProvider.ChromKeys.Count)
{
continue;
}
chromatogramRequestProviders.Add(chromatogramRequestProvider);
}
_chromatogramRequestProviders = chromatogramRequestProviders.ToArray();
_chromTaskLists = new ChromTaskList[_chromatogramRequestProviders.Length];
}
private bool TestChorusAccount(ChorusAccount chorusAccount)
{
using (ChorusSession chorusSession = new ChorusSession(chorusAccount))
{
try
{
CookieContainer cookieContainer = new CookieContainer();
try
{
chorusSession.Login(chorusAccount, cookieContainer);
MessageDlg.Show(this, Resources.EditChorusAccountDlg_TestSettings_Settings_are_correct);
return(true);
}
catch (RemoteServerException chorusException)
{
MessageDlg.ShowException(this, chorusException);
textPassword.Focus();
return(false);
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, Resources.EditChorusAccountDlg_TestSettings_Error_connecting_to_server__ + x.Message, x);
textServerURL.Focus();
return(false);
}
}
}
public bool TestSettings()
{
if (!ValidateValues())
{
return(false);
}
ChorusAccount chorusAccount = GetChorusAccount();
ChorusSession chorusSession = new ChorusSession();
try
{
CookieContainer cookieContainer = new CookieContainer();
try
{
chorusSession.Login(chorusAccount, cookieContainer);
MessageDlg.Show(this, Resources.EditChorusAccountDlg_TestSettings_Settings_are_correct);
return(true);
}
catch (ChorusServerException chorusException)
{
MessageDlg.ShowException(this, chorusException);
textPassword.Focus();
return(false);
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, Resources.EditChorusAccountDlg_TestSettings_Error_connecting_to_server__ + x.Message, x);
textServerURL.Focus();
return(false);
}
}
public EditChorusAccountDlg(ChorusAccount chorusAccount, IEnumerable <ChorusAccount> existing)
{
InitializeComponent();
_existing = ImmutableList.ValueOf(existing);
_originalAccount = chorusAccount;
SetChorusAccount(chorusAccount);
}
//[TestMethod]
public void TestDdaSmall()
{
ChorusAccount TEST_ACCOUNT = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
var stream = typeof (ChromTaskListTest).Assembly.GetManifestResourceStream(typeof (ChromTaskListTest),
"DdaSmall.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequest = (ChromatogramRequestDocument) new XmlSerializer(typeof (ChromatogramRequestDocument)).Deserialize(stream);
var chromTaskList = new ChromTaskList(() => { }, new SrmDocument(SrmSettingsList.GetDefault()), TEST_ACCOUNT,
TEST_ACCOUNT.GetChorusUrl().SetFileId(28836), ChromTaskList.ChunkChromatogramRequest(chromatogramRequest, 100));
chromTaskList.SetMinimumSimultaneousTasks(10);
var failedTasks = new HashSet<ChromatogramGeneratorTask>();
foreach (var chromKey in chromTaskList.ChromKeys)
{
float[] times;
float[] intensities;
float[] massErrors;
int[] scanIds;
chromTaskList.GetChromatogram(chromKey, out times, out scanIds, out intensities, out massErrors);
if (null == times)
{
var task = chromTaskList.GetGeneratorTask(chromKey);
if (failedTasks.Add(task))
{
var memoryStream = new MemoryStream();
var xmlWriter = XmlWriter.Create(memoryStream, new XmlWriterSettings {Encoding = Encoding.UTF8});
new XmlSerializer(typeof(ChromatogramRequestDocument)).Serialize(xmlWriter, task.ChromatogramRequestDocument);
Console.Out.WriteLine("Failed to get data for {0}", Encoding.UTF8.GetString(memoryStream.ToArray()));
}
}
}
Assert.AreEqual(0, failedTasks.Count);
}
//[TestMethod]
public void TestDdaSmall()
{
ChorusAccount TEST_ACCOUNT = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
var stream = typeof(ChromTaskListTest).Assembly.GetManifestResourceStream(typeof(ChromTaskListTest),
"DdaSmall.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequest = (ChromatogramRequestDocument) new XmlSerializer(typeof(ChromatogramRequestDocument)).Deserialize(stream);
var chromTaskList = new ChromTaskList(() => { }, new SrmDocument(SrmSettingsList.GetDefault()), TEST_ACCOUNT,
TEST_ACCOUNT.GetChorusUrl().SetFileId(28836), ChromTaskList.ChunkChromatogramRequest(chromatogramRequest, 100));
chromTaskList.SetMinimumSimultaneousTasks(10);
var failedTasks = new HashSet <ChromatogramGeneratorTask>();
foreach (var chromKey in chromTaskList.ChromKeys)
{
TimeIntensities timeIntensities;
chromTaskList.GetChromatogram(chromKey, out timeIntensities);
if (null == timeIntensities)
{
var task = chromTaskList.GetGeneratorTask(chromKey);
if (failedTasks.Add(task))
{
var memoryStream = new MemoryStream();
var xmlWriter = XmlWriter.Create(memoryStream, new XmlWriterSettings {
Encoding = Encoding.UTF8
});
new XmlSerializer(typeof(ChromatogramRequestDocument)).Serialize(xmlWriter, task.ChromatogramRequestDocument);
Console.Out.WriteLine("Failed to get data for {0}", Encoding.UTF8.GetString(memoryStream.ToArray()));
}
}
}
Assert.AreEqual(0, failedTasks.Count);
}
protected override void DoTest()
{
var chorusAccount = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Hoofnagle_MSe_targeted.sky")));
var importResultsDlg = ShowDialog<ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog<OpenDataSourceDialog>(importResultsDlg.OkDialog);
var multiButtonMsgDlg = ShowDialog<MultiButtonMsgDlg>(() => openDataSourceDialog.CurrentDirectory = ChorusUrl.EMPTY);
OkDialog(multiButtonMsgDlg, multiButtonMsgDlg.Btn1Click);
var editChorusAccountDlg = WaitForOpenForm<EditChorusAccountDlg>();
RunUI(()=>
{
editChorusAccountDlg.SetChorusAccount(chorusAccount);
});
OkDialog(editChorusAccountDlg, editChorusAccountDlg.OkDialog);
Assert.AreEqual(chorusAccount.GetChorusUrl(), openDataSourceDialog.CurrentDirectory);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = chorusAccount.GetChorusUrl().AddPathPart("myFiles");
});
WaitForConditionUI(() => !openDataSourceDialog.WaitingForData);
RunUI(() =>
{
openDataSourceDialog.SelectFile("2013_03_13_UWash_S1_MSE_Adj_001.raw.zip");
openDataSourceDialog.SelectFile("2013_03_13_UWash_S2_MSE_Adj_001.raw.zip");
});
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
ImportResultsNameDlg importResultsNameDlg = WaitForOpenForm<ImportResultsNameDlg>();
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
WaitForConditionUI(() =>
SkylineWindow.DocumentUI.Settings.HasResults &&
SkylineWindow.DocumentUI.Settings.MeasuredResults.IsLoaded
);
Assert.AreEqual(2, SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count);
}
public EditChorusAccountDlg(ChorusAccount chorusAccount, IEnumerable<ChorusAccount> existing)
{
InitializeComponent();
_existing = ImmutableList.ValueOf(existing);
_originalAccount = chorusAccount;
SetChorusAccount(chorusAccount);
}
public ChromatogramGeneratorTask(ChromTaskList chromTaskList, ChorusAccount chorusAccount, ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
ChromTaskList = chromTaskList;
ChorusAccount = chorusAccount;
ChorusUrl = chorusUrl;
ChromatogramRequestDocument = chromatogramRequestDocument;
}
public ChromTaskList(Action checkCancelledAction, SrmDocument srmDocument, ChorusAccount chorusAccount, ChorusUrl chorusUrl, IEnumerable<ChromatogramRequestDocument> chromatogramRequestDocuments)
{
SrmDocument = srmDocument;
ChorusSession = new ChorusSession();
_checkCancelledAction = checkCancelledAction;
_chromatogramGeneratorTasks = new List<ChromatogramGeneratorTask>();
_chromKeys = new Dictionary<ChromKey, ChromatogramGeneratorTask>();
foreach (var chunk in chromatogramRequestDocuments)
{
ChromatogramGeneratorTask task = new ChromatogramGeneratorTask(this, chorusAccount, chorusUrl, chunk);
_chromatogramGeneratorTasks.Add(task);
foreach (ChromKey chromKey in ListChromKeys(chunk))
{
_chromKeys[chromKey] = task;
}
}
_executingTasks = new HashSet<ChromatogramGeneratorTask>();
}
public void TestRemoteAccountList()
{
var unifiAccount = new UnifiAccount("https://unifiserver.xxx", "unifi_username", "unifi_password");
var chorusAccount = new ChorusAccount("https://chorusserver.xxx", "chorus_username", "chorus_password");
var remoteAccountList = new RemoteAccountList();
remoteAccountList.Add(unifiAccount);
remoteAccountList.Add(chorusAccount);
StringWriter stringWriter = new StringWriter();
var xmlSerializer = new XmlSerializer(typeof(RemoteAccountList));
xmlSerializer.Serialize(stringWriter, remoteAccountList);
var serializedAccountList = stringWriter.ToString();
Assert.AreEqual(-1, serializedAccountList.IndexOf(unifiAccount.Password, StringComparison.Ordinal));
Assert.AreEqual(-1, serializedAccountList.IndexOf(chorusAccount.Password, StringComparison.Ordinal));
var roundTrip = (RemoteAccountList)xmlSerializer.Deserialize(new StringReader(serializedAccountList));
Assert.AreEqual(remoteAccountList.Count, roundTrip.Count);
Assert.AreEqual(unifiAccount, roundTrip[0]);
Assert.AreEqual(chorusAccount, roundTrip[1]);
}
protected override void DoTest()
{
var chorusAccount = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Hoofnagle_MSe_targeted.sky")));
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResultsDlg.OkDialog);
var multiButtonMsgDlg = ShowDialog <MultiButtonMsgDlg>(() => openDataSourceDialog.CurrentDirectory = RemoteUrl.EMPTY);
OkDialog(multiButtonMsgDlg, multiButtonMsgDlg.Btn1Click);
var editChorusAccountDlg = WaitForOpenForm <EditRemoteAccountDlg>();
RunUI(() =>
{
editChorusAccountDlg.SetRemoteAccount(chorusAccount);
});
OkDialog(editChorusAccountDlg, editChorusAccountDlg.OkDialog);
Assert.AreEqual(chorusAccount.GetChorusUrl(), openDataSourceDialog.CurrentDirectory);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = chorusAccount.GetChorusUrl().AddPathPart("myFiles");
});
WaitForConditionUI(() => !openDataSourceDialog.WaitingForData);
RunUI(() =>
{
openDataSourceDialog.SelectFile("2013_03_13_UWash_S1_MSE_Adj_001.raw.zip");
openDataSourceDialog.SelectFile("2013_03_13_UWash_S2_MSE_Adj_001.raw.zip");
});
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
ImportResultsNameDlg importResultsNameDlg = WaitForOpenForm <ImportResultsNameDlg>();
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
WaitForConditionUI(() =>
SkylineWindow.DocumentUI.Settings.HasResults &&
SkylineWindow.DocumentUI.Settings.MeasuredResults.IsLoaded
);
Assert.AreEqual(2, SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count);
}
private void populateListViewFromDirectory(MsDataFileUri directory)
{
_abortPopulateList = false;
listView.Cursor = Cursors.Default;
_waitingForData = false;
listView.Items.Clear();
var listSourceInfo = new List <SourceInfo>();
if (null == directory || directory is MsDataFilePath && string.IsNullOrEmpty(((MsDataFilePath)directory).FilePath))
{
foreach (DriveInfo driveInfo in DriveInfo.GetDrives())
{
string label = string.Empty;
string sublabel = driveInfo.Name;
ImageIndex imageIndex = ImageIndex.Folder;
_driveReadiness[sublabel] = false;
try
{
switch (driveInfo.DriveType)
{
case DriveType.Fixed:
imageIndex = ImageIndex.LocalDrive;
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Local_Drive;
if (driveInfo.VolumeLabel.Length > 0)
{
label = driveInfo.VolumeLabel;
}
break;
case DriveType.CDRom:
imageIndex = ImageIndex.OpticalDrive;
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Optical_Drive;
if (driveInfo.IsReady && driveInfo.VolumeLabel.Length > 0)
{
label = driveInfo.VolumeLabel;
}
break;
case DriveType.Removable:
imageIndex = ImageIndex.OpticalDrive;
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Removable_Drive;
if (driveInfo.IsReady && driveInfo.VolumeLabel.Length > 0)
{
label = driveInfo.VolumeLabel;
}
break;
case DriveType.Network:
label = Resources.OpenDataSourceDialog_populateListViewFromDirectory_Network_Share;
break;
}
_driveReadiness[sublabel] = IsDriveReady(driveInfo);
}
catch (Exception)
{
label += string.Format(" ({0})", Resources.OpenDataSourceDialog_populateListViewFromDirectory_access_failure); // Not L10N
}
string name = driveInfo.Name;
if (label != string.Empty)
{
name = string.Format("{0} ({1})", label, name); // Not L10N
}
listSourceInfo.Add(new SourceInfo(new MsDataFilePath(driveInfo.RootDirectory.FullName))
{
type = DataSourceUtil.FOLDER_TYPE,
imageIndex = imageIndex,
name = name,
dateModified = GetDriveModifiedTime(driveInfo)
});
}
}
else if (directory is ChorusUrl)
{
ChorusUrl chorusUrl = directory as ChorusUrl;
if (null == _chorusSession)
{
_chorusSession = new ChorusSession();
_chorusSession.ContentsAvailable += ChorusContentsAvailable;
}
if (string.IsNullOrEmpty(chorusUrl.ServerUrl))
{
foreach (var chorusAccount in _chorusAccounts)
{
listSourceInfo.Add(new SourceInfo(chorusAccount.GetChorusUrl())
{
name = chorusAccount.GetKey(),
type = DataSourceUtil.FOLDER_TYPE,
imageIndex = ImageIndex.Chorus,
});
}
}
else
{
ChorusAccount chorusAccount = GetChorusAccount(chorusUrl);
ChorusServerException exception;
bool isComplete = _chorusSession.AsyncFetchContents(chorusAccount, chorusUrl, out exception);
foreach (var item in _chorusSession.ListContents(chorusAccount, chorusUrl))
{
var imageIndex = DataSourceUtil.IsFolderType(item.Type)
? ImageIndex.Folder
: ImageIndex.MassSpecFile;
listSourceInfo.Add(new SourceInfo(item.ChorusUrl)
{
name = item.Label,
type = item.Type,
imageIndex = imageIndex,
dateModified = item.LastModified,
size = item.FileSize
});
}
if (null != exception)
{
if (MultiButtonMsgDlg.Show(this, exception.Message, Resources.OpenDataSourceDialog_populateListViewFromDirectory_Retry) != DialogResult.Cancel)
{
_chorusSession.RetryFetchContents(chorusAccount, chorusUrl);
isComplete = false;
}
}
if (!isComplete)
{
listView.Cursor = Cursors.WaitCursor;
_waitingForData = true;
}
}
}
else if (directory is MsDataFilePath)
{
MsDataFilePath msDataFilePath = (MsDataFilePath)directory;
DirectoryInfo dirInfo = new DirectoryInfo(msDataFilePath.FilePath);
DirectoryInfo[] arraySubDirInfo;
FileInfo[] arrayFileInfo;
try
{
// subitems: Name, Type, Spectra, Size, Date Modified
arraySubDirInfo = dirInfo.GetDirectories();
Array.Sort(arraySubDirInfo, (d1, d2) => string.Compare(d1.Name, d2.Name, StringComparison.CurrentCultureIgnoreCase));
arrayFileInfo = dirInfo.GetFiles();
Array.Sort(arrayFileInfo, (f1, f2) => string.Compare(f1.Name, f2.Name, StringComparison.CurrentCultureIgnoreCase));
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(
Resources.OpenDataSourceDialog_populateListViewFromDirectory_An_error_occurred_attempting_to_retrieve_the_contents_of_this_directory,
x.Message);
// Might throw access violation.
MessageBox.Show(this, message, Program.Name);
return;
}
// Calculate information about the files, allowing the user to cancel
foreach (var info in arraySubDirInfo)
{
listSourceInfo.Add(getSourceInfo(info));
Application.DoEvents();
if (_abortPopulateList)
{
//MessageBox.Show( "abort" );
break;
}
}
if (!_abortPopulateList)
{
foreach (var info in arrayFileInfo)
{
listSourceInfo.Add(getSourceInfo(info));
Application.DoEvents();
if (_abortPopulateList)
{
//MessageBox.Show( "abort" );
break;
}
}
}
}
// Populate the list
var items = new List <ListViewItem>();
foreach (var sourceInfo in listSourceInfo)
{
if (sourceInfo != null &&
(sourceTypeComboBox.SelectedIndex == 0 ||
sourceTypeComboBox.SelectedItem.ToString() == sourceInfo.type ||
// Always show folders
sourceInfo.isFolder))
{
ListViewItem item = new ListViewItem(sourceInfo.ToArray(), (int)sourceInfo.imageIndex)
{
Tag = sourceInfo,
};
item.SubItems[2].Tag = sourceInfo.size;
item.SubItems[3].Tag = sourceInfo.dateModified;
items.Add(item);
}
}
listView.Items.AddRange(items.ToArray());
}
public void SetChorusAccount(ChorusAccount chorusAccount)
{
textUsername.Text = chorusAccount.Username;
textPassword.Text = chorusAccount.Password;
textServerURL.Text = chorusAccount.ServerUrl;
}
public void SetChorusAccount(ChorusAccount chorusAccount)
{
textUsername.Text = chorusAccount.Username;
textPassword.Text = chorusAccount.Password;
textServerURL.Text = chorusAccount.ServerUrl;
}