private void TestPanoramaServerUrls()
{
var PWEB = "panoramaweb.org";
var PWEB_FULL = "https://panoramaweb.org/";
var PWEB_LK = "panoramaweb.org/labkey";
var PWEB_LK_FULL = "https://panoramaweb.org/labkey/";
var serverUri = PanoramaUtil.ServerNameToUri(PWEB);
var pServer = new PanoramaServer(serverUri, string.Empty, string.Empty);
Assert.AreEqual(pServer.ServerUri.AbsoluteUri, PWEB_FULL);
Assert.IsFalse(pServer.RemoveContextPath());
Assert.IsTrue(pServer.AddLabKeyContextPath());
Assert.AreEqual(pServer.ServerUri.AbsoluteUri, PWEB_LK_FULL);
serverUri = PanoramaUtil.ServerNameToUri(PWEB_LK);
pServer = new PanoramaServer(serverUri, string.Empty, string.Empty);
Assert.AreEqual(pServer.ServerUri.AbsoluteUri, PWEB_LK_FULL);
Assert.IsFalse(pServer.AddLabKeyContextPath());
Assert.IsTrue(pServer.RemoveContextPath());
Assert.AreEqual(pServer.ServerUri.AbsoluteUri, PWEB_FULL);
serverUri = PanoramaUtil.ServerNameToUri(PWEB_LK);
pServer = new PanoramaServer(serverUri, string.Empty, string.Empty);
Assert.AreEqual(pServer.ServerUri, PWEB_LK_FULL);
Assert.IsTrue(pServer.Redirect(PWEB_FULL + PanoramaUtil.ENSURE_LOGIN_PATH,
PanoramaUtil.ENSURE_LOGIN_PATH));
Assert.AreEqual(pServer.ServerUri, PWEB_FULL);
Assert.IsFalse(pServer.Redirect("/labkey/" + PanoramaUtil.ENSURE_LOGIN_PATH, PanoramaUtil.ENSURE_LOGIN_PATH)); // Need full URL
Assert.IsFalse(pServer.Redirect("http:/another.server/" + PanoramaUtil.ENSURE_LOGIN_PATH, PanoramaUtil.ENSURE_LOGIN_PATH)); // Not the same host
}
public static void AddChildContainers(Server server, TreeNode node, JToken folder)
{
JEnumerable <JToken> subFolders = folder["children"].Children(); // Not L10N
foreach (var subFolder in subFolders)
{
string folderName = (string)subFolder["name"]; // Not L10N
TreeNode folderNode = new TreeNode(folderName);
AddChildContainers(server, folderNode, subFolder);
// User can only upload to folders where TargetedMS is an active module.
var canUpload = PanoramaUtil.CheckFolderPermissions(subFolder) && PanoramaUtil.CheckFolderType(subFolder);
// If the user does not have write permissions in this folder or any
// of its subfolders, do not add it to the tree.
if (folderNode.Nodes.Count == 0 && !canUpload)
{
continue;
}
node.Nodes.Add(folderNode);
// User cannot upload files to folder
if (!canUpload)
{
folderNode.ForeColor = Color.Gray;
folderNode.ImageIndex = folderNode.SelectedImageIndex = (int)ImageId.folder;
}
else
{
JToken moduleProperties = subFolder["moduleProperties"]; // Not L10N
if (moduleProperties == null)
{
folderNode.ImageIndex = folderNode.SelectedImageIndex = (int)ImageId.labkey;
}
else
{
string effectiveValue = (string)moduleProperties[0]["effectiveValue"]; // Not L10N
folderNode.ImageIndex =
folderNode.SelectedImageIndex =
(effectiveValue.Equals("Library") || effectiveValue.Equals("LibraryProtein")) // Not L10N
? (int)ImageId.chrom_lib
: (int)ImageId.labkey;
}
}
folderNode.Tag = new FolderInformation(server, canUpload);
}
}
private void PanoramaSetup()
{
Uri serverUri = new Uri(SERVER_URL);
IPanoramaClient panoramaClient = PanoramaUtil.CreatePanoramaClient(serverUri);
var deleteResult = panoramaClient.DeleteFolder($@"{PANORAMA_FOLDER}/{testFolderName}", PANORAMA_USER_NAME,
PANORAMA_PASSWORD);
if (deleteResult != FolderOperationStatus.OK && deleteResult != FolderOperationStatus.notfound)
{
Assert.Fail($@"Cannot delete existing test folder. Returns {deleteResult}");
}
Assert.AreEqual(FolderOperationStatus.OK, panoramaClient.CreateFolder(PANORAMA_FOLDER, testFolderName,
PANORAMA_USER_NAME, PANORAMA_PASSWORD), "Error when creating panorama test folder.");
}
public void OkDialog()
{
MessageBoxHelper helper = new MessageBoxHelper(this);
string serverName;
if (!helper.ValidateNameTextBox(textServerURL, out serverName))
{
return;
}
Uri uriServer = PanoramaUtil.ServerNameToUri(serverName);
if (uriServer == null)
{
helper.ShowTextBoxError(textServerURL, Resources.EditServerDlg_OkDialog_The_text__0__is_not_a_valid_server_name_, serverName);
return;
}
var panoramaClient = PanoramaClient ?? new WebPanoramaClient(uriServer);
using (var waitDlg = new LongWaitDlg {
Text = Resources.EditServerDlg_OkDialog_Verifying_server_information
})
{
try
{
waitDlg.PerformWork(this, 1000, () => PanoramaUtil.VerifyServerInformation(panoramaClient, Username, Password));
}
catch (Exception x)
{
helper.ShowTextBoxError(textServerURL, x.Message);
return;
}
}
Uri updatedUri = panoramaClient.ServerUri ?? uriServer;
if (_existing.Contains(server => !ReferenceEquals(_server, server) && Equals(updatedUri, server.URI)))
{
helper.ShowTextBoxError(textServerURL, Resources.EditServerDlg_OkDialog_The_server__0__already_exists_, uriServer.Host);
return;
}
_server = new Server(updatedUri, Username, Password);
DialogResult = DialogResult.OK;
}
protected override void DoTest()
{
RunUI(() =>
{
SkylineWindow.ResetDefaultSettings();
SkylineWindow.NewDocument();
});
ShowAndPositionAuditLog(false);
PauseForScreenShot <AuditLogForm>("Empty Audit Log form.", 2);
// Configuring Settings for Inserting a New Peptide, p. 3
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
PeptideSettingsUI peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUi);
RunUI(() => peptideSettingsUi.PickedHeavyMods = new[] { modHeavyK.Name });
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with settings modifications.", 4);
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.Width = 1010;
});
PauseForScreenShot("Undo list expanded. (manual)", 4);
RunUI(SkylineWindow.Undo);
PauseForScreenShot("Redo list expanded. (manual)", 5);
RunUI(SkylineWindow.Redo);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
RunUI(pasteDlg.PastePeptides);
RunUI(() =>
{
pasteDlg.Size = new Size(700, 210);
pasteDlg.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
using (new WaitDocumentChange())
{
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
WaitForConditionUI(() => SkylineWindow.SequenceTree.Nodes.Count > 0);
}
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Height = 390;
});
PauseForScreenShot("Main window with Targets view", 6);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with inserted peptide.", 7);
ShowLastExtraInfo("Extra info form with inserted peptide info.", 7);
string documentPath = GetTestPath("AuditLogTutorial" + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentPath));
WaitForCondition(() => File.Exists(documentPath));
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value;
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
OkDialog(importResultsDlg, importResultsDlg.OkDialog);
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(9, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <AuditLogForm>("Audit Log form with imported data files.", 9);
ShowLastExtraInfo("Extra info form for the import.", 9);
// Peptide Quantitification Settings p. 9
peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = (PeptideSettingsUI.TABS) 5);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with quantification settings.", 10);
// Specify analyte concentrations of external standards
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.ShowDocumentGrid(true);
});
var documentGridForm = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
string pasteString = TextUtil.LineSeparate(concentrations.Select((f, i) =>
QuantificationStrings.SampleType_STANDARD_Standard + "\t" + f));
ClipboardEx.SetText(pasteString);
using (new WaitDocumentChange())
{
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.CurrentCell = documentGridForm.DataGridView.Rows[1].Cells[colSampleType.Index];
documentGridForm.DataGridView.SendPaste();
});
}
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var gridFloatingWindow = documentGridForm.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 315);
gridFloatingWindow.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <DocumentGridForm>("Document grid with concentrations filled in", 11);
RunUI(documentGridForm.Close);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with grid changes", 12);
ShowLastExtraInfo("Extra Info for the analyte data import.", 12);
RunUI(SkylineWindow.AuditLogForm.Close);
const string unknownReplicate = "FOXN1-GST";
RestoreViewOnScreen(13);
ActivateReplicate(unknownReplicate);
SelectNode(SrmDocument.Level.TransitionGroups, 1);
RunUI(() => SkylineWindow.Size = new Size(936, 527));
WaitForGraphs();
PauseForScreenShot("Heavy precursor chromatogram", 13);
RunUI(() =>
{
var pathHeavy = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1);
var graphChrom = SkylineWindow.GetGraphChrom(unknownReplicate);
Assert.IsNotNull(graphChrom);
Assert.AreEqual(unknownReplicate, graphChrom.NameSet);
var firstGroupInfo = graphChrom.ChromGroupInfos.FirstOrDefault();
Assert.IsNotNull(firstGroupInfo, "Missing group info");
var firstChromItem = graphChrom.GraphItems.FirstOrDefault(gci => gci.TransitionChromInfo != null);
Assert.IsNotNull(firstChromItem, "Missing graph item");
var listChanges = new List <ChangedPeakBoundsEventArgs>
{
new ChangedPeakBoundsEventArgs(pathHeavy,
null,
graphChrom.NameSet,
firstGroupInfo.FilePath,
firstChromItem.GetValidPeakBoundaryTime(20.65),
firstChromItem.GetValidPeakBoundaryTime(21.15),
PeakIdentification.FALSE,
PeakBoundsChangeType.both)
};
graphChrom.SimulateChangedPeakBounds(listChanges);
});
ShowAndPositionAuditLog(true, 50, 200);
WaitForConditionUI(500, () => SkylineWindow.AuditLogForm.DataGridView.Rows.Count > 0);
PauseForScreenShot <AuditLogForm>("Audit Log form with changed integration boundary.", 14);
int reasonIndex = 2;
using (new WaitDocumentChange())
{
RunUI(() =>
{
var pathReason = PropertyPath.Root.Property("Reason");
var colReason = SkylineWindow.AuditLogForm.FindColumn(pathReason);
reasonIndex = colReason.Index;
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex,
"Changed peak integration as instructed by the tutorial");
});
}
RunUI(() => SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex));
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
PauseForScreenShot <AuditLogForm>("Audit Log form with updated reason.", 14);
// View the calibration curve p. 15
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
var priorZoomState = ZoomCalibrationCurve(calibrationForm, 0.52);
RunUI(() =>
{
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
VerifyCalibrationCurve(calibrationForm, 5.4065E-1, -2.9539E-1, 0.999);
});
PauseForScreenShot <CalibrationForm>("Calibration curve zoomed", 15);
RunUI(() =>
{
priorZoomState?.ApplyState(calibrationForm.ZedGraphControl.GraphPane);
var chromatograms = SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms;
new [] { 5, 6, 7, 8 }.ForEach((index) =>
{
int replicateIdx = chromatograms.IndexOf((ch) => ch.Name.Equals("Standard_" + index));
Assert.IsTrue(replicateIdx >= 0);
using (var excludeStandardMenu = calibrationForm.MakeExcludeStandardMenuItem(replicateIdx))
{
excludeStandardMenu?.PerformClick();
}
});
});
WaitForGraphs();
RunUI(() => VerifyCalibrationCurve(calibrationForm, 5.52E-1, -6.3678E-1, 1));
OkDialog(calibrationForm, calibrationForm.Close);
PauseForScreenShot <AuditLogForm>("Audit Log with excluded standard records", 16);
PauseForScreenShot <AuditLogForm>("Audit Log Reports menu (manual)", 16);
// TODO(nicksh): Audit log reason field does not currently support fill down
// RunUI(() =>
// {
// SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex, "Excluded standard below LOD");
// for (int i = 0; i < 4; i++)
// SkylineWindow.AuditLogForm.DataGridView.Rows[i].Cells[reasonIndex].Selected = true;
// });
// RunUI(() => SkylineWindow.AuditLogForm.DataboundGridControl.FillDown());
RunUI(() =>
{
for (int i = 0; i < 4; i++)
{
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, i, reasonIndex, "Excluded standard below LOD");
}
});
RunUI(() =>
{
SkylineWindow.AuditLogForm.ChooseView(AuditLogStrings.AuditLogForm_MakeAuditLogForm_Undo_Redo);
});
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() =>
{
var floatingWindow = SkylineWindow.AuditLogForm.Parent.Parent;
floatingWindow.Height = 334;
floatingWindow.Width -= 15;
});
PauseForScreenShot <AuditLogForm>("Audit Log with UndoRedo view.", 17);
if (IsCoverShotMode)
{
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
var calibrationCoverForm = WaitForOpenForm <CalibrationForm>();
ZoomCalibrationCurve(calibrationCoverForm, 0.53);
var floatingLogWindow = SkylineWindow.AuditLogForm.Parent.Parent;
var floatingCalWindow = calibrationCoverForm.Parent.Parent;
RunUI(() =>
{
floatingLogWindow.Top = SkylineWindow.Bottom - floatingLogWindow.Height - 8;
floatingLogWindow.Left =
(SkylineWindow.Left + SkylineWindow.Right) / 2 - floatingLogWindow.Width / 2;
floatingCalWindow.Top = SkylineWindow.Top + 8;
floatingCalWindow.Left = SkylineWindow.Right - floatingCalWindow.Width - 8;
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex);
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex - 1);
});
TakeCoverShot();
}
var customizeDialog = ShowDialog <ViewEditor>(SkylineWindow.AuditLogForm.NavBar.CustomizeView);
RunUI(() =>
{
customizeDialog.ViewName = "Custom Columns";
var columnsToAdd = new[]
{
PropertyPath.Parse("SkylineVersion"),
PropertyPath.Parse("User"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(customizeDialog.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
customizeDialog.ChooseColumnsTab.AddSelectedColumn();
}
customizeDialog.Height = 370;
});
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Custom Columns report template", 17);
OkDialog(customizeDialog, customizeDialog.OkDialog);
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() => SkylineWindow.AuditLogForm.Parent.Parent.Height += 10); // Extra for 2-line headers
PauseForScreenShot <AuditLogForm>("Audit Log with custom view.", 18);
var registrationDialog = ShowDialog <MultiButtonMsgDlg>(() => SkylineWindow.ShowPublishDlg(null));
PauseForScreenShot <MultiButtonMsgDlg>("Upload confirmation dialog.", 19);
var loginDialog = ShowDialog <EditServerDlg>(registrationDialog.ClickNo);
PauseForScreenShot <EditServerDlg>("Login dialog.", 20);
RunUI(() =>
{
loginDialog.URL = SERVER_URL;
loginDialog.Username = PANORAMA_USER_NAME;
});
if (!IsPauseForScreenShots)
{
OkDialog(loginDialog, loginDialog.CancelButton.PerformClick);
}
else
{
PauseTest("Enter password. (manual) No screen shot.");
var publishDialog = ShowDialog <PublishDocumentDlg>(loginDialog.OkDialog);
WaitForCondition(() => publishDialog.IsLoaded);
RunUI(() =>
{
publishDialog.SelectItem(testFolderName);
});
PauseForScreenShot <PublishDocumentDlg>("Folder selection dialog.", 21);
var browserConfirmationDialog = ShowDialog <MultiButtonMsgDlg>(publishDialog.OkDialog);
OkDialog(browserConfirmationDialog, browserConfirmationDialog.ClickYes);
PauseForScreenShot("Uploaded document in Panorama (in browser).");
Regex reDocId = new Regex(@"\?id=([0-9]+)");
Assert.IsTrue(reDocId.IsMatch(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()));
string docId = reDocId.Match(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()).Groups[1].Captures[0].Value;
Uri serverUri = new Uri(SERVER_URL);
Uri requestUri = PanoramaUtil.Call(serverUri, "targetedms", String.Format("{0}/{1}", PANORAMA_FOLDER, testFolderName),
"showSkylineAuditLog", "id=" + docId);
Process.Start(requestUri.ToString());
PauseForScreenShot("Uploaded document audit log in Panorama (in browser).");
}
}
