public void ImportMultipleFilesOnOpen()
{
// get settings in a separate invocation because import starts immediately when a file is passed on the command-line
var settings = TestContext.GetAndSetTestSettings();
// this lambda allow reusing of the testing code; we can change only UI parameters to create a specific AppRunner
Func <string, AppRunner> createTestCase = (mergedOutputFilepath) =>
{
return((app, windowStack) =>
{
var window = app.GetWindow(SearchCriteria.ByAutomationId("IDPickerForm"), InitializeOption.NoCache);
var statusBar = window.Get <StatusStrip>();
var statusText = statusBar.Get <TextBox>();
windowStack.Push(window);
if (String.IsNullOrEmpty(mergedOutputFilepath))
{
// check:
// - trying to save to a read only location prompts for a new location
// - choosing an existing filepath asks user to confirm overwriting
// - that the automatically generated merged filepath is correct
Window saveDialog = null;
IDPicker.Util.TryRepeatedly(() => saveDialog = window.ModalWindows()[0]);
windowStack.Push(saveDialog);
// HACK: saveDialog.Get<TextBox>() won't work because of some unsupported control types in the Save Dialog (at least on Windows 7); I'm not sure if the 1001 id is stable
var saveTarget = new TextBox(saveDialog.AutomationElement.FindFirst(TreeScope.Descendants, new PropertyCondition(AutomationElement.AutomationIdProperty, "1001")), new NullActionListener());
Assert.AreEqual(TestContext.TestOutputPath("201208-378803.idpDB"), saveTarget.Text);
var saveButton = new Button(saveDialog.AutomationElement.FindFirst(TreeScope.Descendants, new PropertyCondition(AutomationElement.AutomationIdProperty, "1")), new NullActionListener());
saveButton.Click();
}
var progressForm = window.ModalWindow(SearchCriteria.ByAutomationId("ProgressForm"), InitializeOption.NoCache);
windowStack.Push(progressForm);
var importSettings = window.ModalWindow(SearchCriteria.ByAutomationId("UserDialog"));
windowStack.Push(importSettings);
var settingsTable = importSettings.GetFastTable("dataGridView");
Assert.IsNotNull(settingsTable);
Assert.AreEqual(4, settingsTable.Rows.Count);
Assert.AreEqual(7, settingsTable.Rows[0].Cells.Count);
UnitTestExtensions.AssertSequenceEquals(new Object[] { "Comet 2014.02", FilepathOrFilename(settingsTable.Rows[0].Cells[1].Value.ToString()), "XXX_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "Comet optimized" }, settingsTable.Rows[0].Cells.Select(o => o.Value).ToArray());
UnitTestExtensions.AssertSequenceEquals(new Object[] { "MyriMatch 2.2.140", FilepathOrFilename(settingsTable.Rows[1].Cells[1].Value.ToString()), "XXX_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "MyriMatch optimized" }, settingsTable.Rows[1].Cells.Select(o => o.Value).ToArray());
UnitTestExtensions.AssertSequenceEquals(new Object[] { "MS-GF+ Beta (v10072)", FilepathOrFilename(settingsTable.Rows[2].Cells[1].Value.ToString()), "XXX", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "MS-GF+" }, settingsTable.Rows[2].Cells.Select(o => o.Value).ToArray());
UnitTestExtensions.AssertSequenceEquals(new Object[] { "Mascot 2.2.06", "cow.protein.PRG2012-subset.fasta", "DECOY_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "Mascot ionscore" }, settingsTable.Rows[3].Cells.Select(o => o.Value).ToArray());
// HACK: for some reason White's TableCell.Value property isn't sending keyboard input correctly;
// with this workaround, be careful while debugging around this code because the keyboard input might be sent to the debugger!
settingsTable.Rows[0].Cells[1].Click();
importSettings.Keyboard.Enter(TestContext.TestDataFilePath("cow.protein.PRG2012-subset.fasta"));
// TODO: add interface testing
// test qonverter settings
// test error conditions (bad values for max rank and max FDR score)
// test invalid decoy prefix
// test analysis parameters tree
var ok = importSettings.Get <Button>("okButton");
ok.RaiseClickEvent();
windowStack.Pop();
while (!progressForm.IsClosed)
{
Thread.Sleep(500);
}
windowStack.Pop();
bool willEmbedGeneMetadata = settings.GUISettings.WarnAboutNoGeneMetadata;
// handle prompt for gene metadata embedding if necessary
if (willEmbedGeneMetadata)
{
var prompt = window.ModalWindow(SearchCriteria.ByAutomationId("EmbedGeneMetadataWarningForm"), InitializeOption.NoCache);
windowStack.Push(prompt);
prompt.Get <CheckBox>("doNotShowCheckBox").Click();
prompt.Get <Button>("embedButton").RaiseClickEvent();
while (!prompt.IsClosed)
{
Thread.Sleep(500);
}
// refresh settings
settings = app.GetSettings(windowStack);
Assert.AreEqual(false, settings.GUISettings.WarnAboutNoGeneMetadata);
// reset to original state
settings.GUISettings.WarnAboutNoGeneMetadata = true;
app.SetSettings(windowStack, settings);
}
statusText.WaitForReady();
window = app.GetWindow(SearchCriteria.ByAutomationId("IDPickerForm"), InitializeOption.NoCache);
var dockableForms = window.GetDockableForms();
var proteinTableForm = dockableForms.Single(o => o.Id == "ProteinTableForm");
if (willEmbedGeneMetadata)
{
Assert.AreEqual("Protein View: 6 clusters, 8 protein groups, 13 proteins, 0% protein FDR, 8 gene groups, 13 genes", proteinTableForm.Name);
}
else
{
Assert.AreEqual("Protein View: 6 clusters, 8 protein groups, 13 proteins, 0% protein FDR", proteinTableForm.Name);
}
var peptideTableForm = dockableForms.Single(o => o.Id == "PeptideTableForm");
Assert.AreEqual("Peptide View: 43 distinct peptides, 47 distinct matches", peptideTableForm.Name);
var spectrumTableForm = dockableForms.Single(o => o.Id == "SpectrumTableForm");
Assert.AreEqual("Spectrum View: 1 groups, 1 sources, 42 spectra", spectrumTableForm.Name);
var modificationTableForm = dockableForms.Single(o => o.Id == "ModificationTableForm");
Assert.AreEqual("Modification View: 24 modified spectra", modificationTableForm.Name);
var analysisTableForm = dockableForms.Single(o => o.Id == "AnalysisTableForm");
Assert.AreEqual("Analysis View", analysisTableForm.Name);
var filterHistoryForm = dockableForms.Single(o => o.Id == "FilterHistoryForm");
Assert.AreEqual("Filter History", filterHistoryForm.Name);
});
};
// make sure embed gene metadata warning is turned on for first tests
if (!settings.GUISettings.WarnAboutNoGeneMetadata)
{
settings.GUISettings.WarnAboutNoGeneMetadata = true;
TestContext.SetSettings(settings);
}
var inputFiles = new string[] { "201208-378803-*.mzid", "201208-378803-*xml", "F003098.dat" };
TestOutputSubdirectory = TestContext.TestName + "-EmbedGeneMetadata";
TestContext.CopyTestInputFiles(inputFiles);
TestContext.LaunchAppTest("IDPicker.exe", TestContext.TestOutputPath("*.*").QuotePathWithSpaces() + " --test-ui-layout", createTestCase(""), closeAppOnError: true);
TestOutputSubdirectory = TestContext.TestName + "-EmbedGeneMetadata-MergedOutputFilepath";
TestContext.CopyTestInputFiles(inputFiles);
TestContext.LaunchAppTest("IDPicker.exe", TestContext.TestOutputPath("*.*").QuotePathWithSpaces() + " -MergedOutputFilepath foobar.idpDB --test-ui-layout", createTestCase("foobar.idpDB"), closeAppOnError: true);
settings.GUISettings.WarnAboutNoGeneMetadata = false;
TestContext.SetSettings(settings);
TestOutputSubdirectory = TestContext.TestName + "-MergedOutputFilepath";
TestContext.CopyTestInputFiles(inputFiles);
TestContext.LaunchAppTest("IDPicker.exe", TestContext.TestOutputPath("*.*").QuotePathWithSpaces() + " -MergedOutputFilepath foobar.idpDB --test-ui-layout", createTestCase("foobar.idpDB"), closeAppOnError: true);
}
public void ImportMultipleFilesFromMenu()
{
IDPickerAllSettings settings = null;
Func <AppRunner> createTestCase = () =>
{
return((app, windowStack) =>
{
var window = app.GetWindow(SearchCriteria.ByAutomationId("IDPickerForm"), InitializeOption.NoCache);
var statusBar = window.Get <StatusStrip>();
var statusText = statusBar.Get <TextBox>();
windowStack.Push(window);
settings = app.GetAndSetTestSettings(windowStack);
var menu = window.RawGet <MenuBar>(SearchCriteria.ByAutomationId("menuStrip1"), 2);
//menu.MenuItemBy(SearchCriteria.ByAutomationId("toolsToolStripMenuItem"), SearchCriteria.ByAutomationId("optionsToolStripMenuItem")).Click();
menu.MenuItem("File", "Import files").Click(); // FIXME: not localized, but the AutomationIds aren't being set properly so the above line won't work
var importFilesForm = window.ModalWindow(SearchCriteria.ByAutomationId("IDPOpenDialog"), InitializeOption.WithCache);
windowStack.Push(importFilesForm);
// make sure "all importable IDPicker formats" is selected, should be the first option
var sourceType = importFilesForm.Get <ComboBox>("sourceTypeComboBox");
sourceType.Select(0);
var fileTree = importFilesForm.Get <Tree>(SearchCriteria.ByAutomationId("FileTree"));
List <string> pathSegments = TestContext.TestOutputPath().Split('\\').ToList();
pathSegments[0] += '\\';
var node = fileTree.Node(pathSegments.ToArray());
node.Select();
importFilesForm.Get <Button>("AddNode").Click(); // TODO: fix variable names in Jay's code to be consistent with my code
Thread.Sleep(500);
importFilesForm.Get <Button>("openButton").RaiseClickEvent();
window.WaitWhileBusy();
// check:
// - trying to save to a read only location prompts for a new location
// - choosing an existing filepath asks user to confirm overwriting
// - that the automatically generated merged filepath is correct
Window saveDialog = null;
IDPicker.Util.TryRepeatedly <ArgumentOutOfRangeException>(() => saveDialog = window.ModalWindows()[0], 10, 500);
windowStack.Push(saveDialog);
// HACK: saveDialog.Get<TextBox>() won't work because of some unsupported control types in the Save Dialog (at least on Windows 7); I'm not sure if the 1001 id is stable
var saveTarget = new TextBox(saveDialog.AutomationElement.FindFirst(TreeScope.Descendants, new PropertyCondition(AutomationElement.AutomationIdProperty, "1001")), new NullActionListener());
Assert.AreEqual(TestContext.TestOutputPath("201208-378803.idpDB"), saveTarget.Text);
var saveButton = new Button(saveDialog.AutomationElement.FindFirst(TreeScope.Descendants, new PropertyCondition(AutomationElement.AutomationIdProperty, "1")), new NullActionListener());
saveButton.Click();
windowStack.Pop();
var progressForm = window.ModalWindow(SearchCriteria.ByAutomationId("ProgressForm"), InitializeOption.NoCache);
windowStack.Push(progressForm);
var importSettings = window.ModalWindow(SearchCriteria.ByAutomationId("UserDialog"));
windowStack.Push(importSettings);
var settingsTable = importSettings.GetFastTable("dataGridView");
Assert.IsNotNull(settingsTable);
Assert.AreEqual(4, settingsTable.Rows.Count);
Assert.AreEqual(7, settingsTable.Rows[0].Cells.Count);
UnitTestExtensions.AssertSequenceEquals(new Object[] { "Comet 2014.02", FilepathOrFilename(settingsTable.Rows[0].Cells[1].Value.ToString()), "XXX_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "Comet optimized" }, settingsTable.Rows[0].Cells.Select(o => o.Value).ToArray());
UnitTestExtensions.AssertSequenceEquals(new Object[] { "MyriMatch 2.2.140", FilepathOrFilename(settingsTable.Rows[1].Cells[1].Value.ToString()), "XXX_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "MyriMatch optimized" }, settingsTable.Rows[1].Cells.Select(o => o.Value).ToArray());
UnitTestExtensions.AssertSequenceEquals(new Object[] { "MS-GF+ Beta (v10072)", FilepathOrFilename(settingsTable.Rows[2].Cells[1].Value.ToString()), "XXX", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "MS-GF+" }, settingsTable.Rows[2].Cells.Select(o => o.Value).ToArray());
UnitTestExtensions.AssertSequenceEquals(new Object[] { "Mascot 2.2.06", "cow.protein.PRG2012-subset.fasta", "DECOY_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "Mascot ionscore" }, settingsTable.Rows[3].Cells.Select(o => o.Value).ToArray());
// HACK: for some reason White's TableCell.Value property isn't sending keyboard input correctly;
// with this workaround, be careful while debugging around this code because the keyboard input might be sent to the debugger!
settingsTable.Rows[0].Cells[1].Click();
importSettings.Keyboard.Enter(TestContext.TestDataFilePath("cow.protein.PRG2012-subset.fasta"));
// TODO: add interface testing
// test qonverter settings
// test error conditions (bad values for max rank and max FDR score)
// test invalid decoy prefix
// test analysis parameters tree
var ok = importSettings.Get <Button>("okButton");
ok.Click();
windowStack.Pop();
while (!progressForm.IsClosed)
{
Thread.Sleep(1000);
}
windowStack.Pop();
if (settings.GUISettings.WarnAboutNoGeneMetadata)
{
// handle prompt for gene metadata embedding
var prompt = window.ModalWindow(SearchCriteria.ByAutomationId("EmbedGeneMetadataWarningForm"), InitializeOption.NoCache);
prompt.Get <Button>("embedButton").RaiseClickEvent();
}
statusText.WaitForReady();
window = app.GetWindow(SearchCriteria.ByAutomationId("IDPickerForm"), InitializeOption.NoCache);
var dockableForms = window.GetDockableForms();
var proteinTableForm = dockableForms.Single(o => o.Id == "ProteinTableForm");
if (settings.GUISettings.WarnAboutNoGeneMetadata)
{
Assert.AreEqual("Protein View: 6 clusters, 8 protein groups, 13 proteins, 0% protein FDR, 8 gene groups, 13 genes", proteinTableForm.Name);
}
else
{
Assert.AreEqual("Protein View: 6 clusters, 8 protein groups, 13 proteins, 0% protein FDR", proteinTableForm.Name);
}
var peptideTableForm = dockableForms.Single(o => o.Id == "PeptideTableForm");
Assert.AreEqual("Peptide View: 43 distinct peptides, 47 distinct matches", peptideTableForm.Name);
var spectrumTableForm = dockableForms.Single(o => o.Id == "SpectrumTableForm");
Assert.AreEqual("Spectrum View: 2 groups, 1 sources, 42 spectra", spectrumTableForm.Name);
var modificationTableForm = dockableForms.Single(o => o.Id == "ModificationTableForm");
Assert.AreEqual("Modification View: 24 modified spectra", modificationTableForm.Name);
var analysisTableForm = dockableForms.Single(o => o.Id == "AnalysisTableForm");
Assert.AreEqual("Analysis View", analysisTableForm.Name);
var filterHistoryForm = dockableForms.Single(o => o.Id == "FilterHistoryForm");
Assert.AreEqual("Filter History", filterHistoryForm.Name);
});
};
TestContext.CopyTestInputFiles("201208-378803*.pepXML", "201208-378803*.pep.xml", "201208-378803*.mzid", "F003098.dat");
TestContext.LaunchAppTest("IDPicker.exe", "--test-ui-layout", createTestCase(), closeAppOnError: true);
// toggle embed gene metadata warning
settings.GUISettings.WarnAboutNoGeneMetadata = !settings.GUISettings.WarnAboutNoGeneMetadata;
TestContext.SetSettings(settings);
// delete the idpDB files between tests
Directory.GetFiles(TestContext.TestOutputPath(), "*.idpDB").ToList().ForEach(o => File.Delete(o));
TestContext.LaunchAppTest("IDPicker.exe", "--test-ui-layout", createTestCase(), closeAppOnError: true);
// test with default hierarchy when input is a flat hierarchy, e.g. /source1, /source2; should be no groups in output
// test with default hierarchy when input is a multi-level hierarchy, e.g. /A/1/source1, /B/2/source2; the hierarchy should be preserved in the output
// test that sources are combined together when they are in separate places in the filesystem, even Mascot DAT files
// test that files are combined properly when
}
public void ImportSingleFileOnOpen()
{
// get settings in a separate invocation because import starts immediately when a file is passed on the command-line
var settings = TestContext.GetAndSetTestSettings();
// this lambda allow reusing of the testing code; we can change only UI parameters to create a specific AppRunner
Func <AppRunner> createTestCase = () =>
{
return((app, windowStack) =>
{
var window = app.GetWindow(SearchCriteria.ByAutomationId("IDPickerForm"), InitializeOption.NoCache);
var statusBar = window.Get <StatusStrip>();
var statusText = statusBar.Get <TextBox>();
windowStack.Push(window);
var progressForm = window.ModalWindow(SearchCriteria.ByAutomationId("ProgressForm"), InitializeOption.NoCache);
windowStack.Push(progressForm);
var importSettings = window.ModalWindow("Import Settings"); // TODO: don't use Text
windowStack.Push(importSettings);
var settingsTable = importSettings.GetFastTable("dataGridView");
Assert.IsNotNull(settingsTable);
Assert.AreEqual(1, settingsTable.Rows.Count);
var firstRow = settingsTable.Rows[0];
Assert.AreEqual(7, settingsTable.Rows[0].Cells.Count);
UnitTestExtensions.AssertSequenceEquals(new Object[] { "MyriMatch 2.2.140", "cow.protein.PRG2012-subset.fasta", "XXX_", "2", 0.1m.ToString(CultureInfo.CurrentCulture), "False", "MyriMatch optimized" }, settingsTable.Rows[0].Cells.Select(o => o.Value).ToArray());
// HACK: for some reason White's TableCell.Value property isn't sending keyboard input correctly;
// with this workaround, be careful while debugging around this code because the keyboard input might be sent to the debugger!
settingsTable.Rows[0].Cells[1].Click();
importSettings.Keyboard.Enter(TestContext.TestDataFilePath("cow.protein.PRG2012-subset.fasta"));
// TODO: add interface testing
// test qonverter settings
// test error conditions (bad values for max rank and max FDR score)
// test invalid decoy prefix
// test analysis parameters tree
var ok = importSettings.Get <Button>("okButton");
ok.Click();
windowStack.Pop();
while (!progressForm.IsClosed)
{
Thread.Sleep(500);
}
windowStack.Pop();
bool willEmbedGeneMetadata = settings.GUISettings.WarnAboutNoGeneMetadata;
// handle prompt for gene metadata embedding if necessary
if (settings.GUISettings.WarnAboutNoGeneMetadata)
{
var prompt = window.ModalWindow(SearchCriteria.ByAutomationId("EmbedGeneMetadataWarningForm"), InitializeOption.NoCache);
windowStack.Push(prompt);
prompt.Get <CheckBox>("doNotShowCheckBox").Click();
prompt.Get <Button>("embedButton").RaiseClickEvent();
while (!prompt.IsClosed)
{
Thread.Sleep(500);
}
// refresh settings
settings = app.GetSettings(windowStack);
Assert.AreEqual(false, settings.GUISettings.WarnAboutNoGeneMetadata);
// reset to original state
settings.GUISettings.WarnAboutNoGeneMetadata = true;
app.SetSettings(windowStack, settings);
}
statusText.WaitForReady();
window = app.GetWindow(SearchCriteria.ByAutomationId("IDPickerForm"), InitializeOption.NoCache);
var dockableForms = window.GetDockableForms();
var proteinTableForm = dockableForms.Single(o => o.Id == "ProteinTableForm");
if (willEmbedGeneMetadata)
{
Assert.AreEqual("Protein View: 9 clusters, 9 protein groups, 19 proteins, 0% protein FDR, 9 gene groups, 19 genes", proteinTableForm.Name);
}
else
{
Assert.AreEqual("Protein View: 9 clusters, 9 protein groups, 19 proteins, 0% protein FDR", proteinTableForm.Name);
}
var peptideTableForm = dockableForms.Single(o => o.Id == "PeptideTableForm");
Assert.AreEqual("Peptide View: 129 distinct peptides, 191 distinct matches", peptideTableForm.Name);
var spectrumTableForm = dockableForms.Single(o => o.Id == "SpectrumTableForm");
Assert.AreEqual("Spectrum View: 1 groups, 1 sources, 207 spectra", spectrumTableForm.Name);
var modificationTableForm = dockableForms.Single(o => o.Id == "ModificationTableForm");
Assert.AreEqual("Modification View: 82 modified spectra", modificationTableForm.Name);
var analysisTableForm = dockableForms.Single(o => o.Id == "AnalysisTableForm");
Assert.AreEqual("Analysis View", analysisTableForm.Name);
var filterHistoryForm = dockableForms.Single(o => o.Id == "FilterHistoryForm");
Assert.AreEqual("Filter History", filterHistoryForm.Name);
});
};
// make sure embed gene metadata warning is turned on for first tests
if (!settings.GUISettings.WarnAboutNoGeneMetadata)
{
settings.GUISettings.WarnAboutNoGeneMetadata = true;
TestContext.SetSettings(settings);
}
var inputFiles = new string[] { "201203-624176-12-mm.pepXML" };
TestOutputSubdirectory = TestContext.TestName + "-EmbedGeneMetadata";
TestContext.CopyTestInputFiles(inputFiles);
TestContext.LaunchAppTest("IDPicker.exe", TestContext.TestOutputPath("*.*").QuotePathWithSpaces() + " --test-ui-layout", createTestCase(), closeAppOnError: true);
settings.GUISettings.WarnAboutNoGeneMetadata = false;
TestContext.SetSettings(settings);
TestOutputSubdirectory = TestContext.TestName;
TestContext.CopyTestInputFiles(inputFiles);
TestContext.LaunchAppTest("IDPicker.exe", TestContext.TestOutputPath("*.*").QuotePathWithSpaces() + " --test-ui-layout", createTestCase(), closeAppOnError: true);
}
