public Schema(ISessionFactory sessionFactory, DataSettings dataSettings)
{
_sessionFactory = sessionFactory;
_annotationDefNames = new HashSet <string>();
if (dataSettings != null)
{
foreach (var annotationDef in dataSettings.AnnotationDefs)
{
_annotationDefNames.Add(AnnotationDef.GetKey(annotationDef.Name));
}
}
}
private void ZipTestAnnotations()
{
var sampleId = new AnnotationDef("SampleID", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.replicate),
AnnotationDef.AnnotationType.text,
new List <string>());
var isConc = new AnnotationDef("IS Conc", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.replicate),
AnnotationDef.AnnotationType.text,
new List <string>());
var analyteConcentration = new AnnotationDef("Analyte Concentration", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.replicate),
AnnotationDef.AnnotationType.text,
new List <string>());
var sampleIdTransition = new AnnotationDef("SampleID", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.transition),
AnnotationDef.AnnotationType.text,
new List <string>());
// Test proper loading of annotations
string testAnnotationsPath = TestFilesDir.GetTestPath("TestAnnotations.zip"); // Not L10N
RunDlg <ConfigureToolsDlg>(() => SkylineWindow.ShowConfigureToolsDlg(), dlg =>
{
dlg.RemoveAllTools();
dlg.InstallZipTool(testAnnotationsPath);
WaitForConditionUI(3 * 1000, () => dlg.ToolList.Count == 4);
ToolDescription t0 = dlg.ToolList[0];
ToolDescription t1 = dlg.ToolList[1];
ToolDescription t2 = dlg.ToolList[2];
ToolDescription t3 = dlg.ToolList[3];
AssertEx.AreEqualDeep(t0.Annotations, new List <AnnotationDef>());
AssertEx.AreEqualDeep(t1.Annotations,
new List <AnnotationDef>
{
sampleId,
isConc,
analyteConcentration
});
AssertEx.AreEqualDeep(t2.Annotations, new List <AnnotationDef> {
sampleId
});
AssertEx.AreEqualDeep(t3.Annotations, new List <AnnotationDef>());
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(sampleId));
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(isConc));
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(analyteConcentration));
dlg.OkDialog();
});
// Test conflicting annotations
var configureToolsDlg = ShowDialog <ConfigureToolsDlg>(SkylineWindow.ShowConfigureToolsDlg);
string conflictAnnotationsPath = TestFilesDir.GetTestPath("ConflictAnnotations.zip"); // Not L10N
RunDlg <MultiButtonMsgDlg>(() => configureToolsDlg.InstallZipTool(conflictAnnotationsPath),
messageDlg => messageDlg.Btn1Click()); // keep existing annotations
WaitForConditionUI(3 * 1000, () => configureToolsDlg.ToolList.Count == 5);
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(sampleId));
RunDlg <MultiButtonMsgDlg>(() => configureToolsDlg.InstallZipTool(conflictAnnotationsPath),
dlg => dlg.Btn0Click());
{
var messageDlg = WaitForOpenForm <MultiButtonMsgDlg>();
OkDialog(messageDlg, messageDlg.Btn0Click);
}
// overwrite existing annotations
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(sampleIdTransition));
OkDialog(configureToolsDlg, configureToolsDlg.OkDialog);
RunUI(() => SkylineWindow.PopulateToolsMenu());
// Test running the tool with an unchecked annotation
RunDlg <MessageDlg>(() => SkylineWindow.RunTool(4), dlg =>
{
Assert.AreEqual(TextUtil.LineSeparate(Resources.ToolDescription_VerifyAnnotations_This_tool_requires_the_use_of_the_following_annotations_which_are_not_enabled_for_this_document,
string.Empty,
TextUtil.LineSeparate(new Collection <string> {
sampleId.GetKey()
}),
string.Empty,
Resources.ToolDescription_VerifyAnnotations_Please_enable_these_annotations_and_fill_in_the_appropriate_data_in_order_to_use_the_tool_), dlg.Message);
dlg.OkDialog();
});
// Test running the tool with a missing annotation
Settings.Default.AnnotationDefList = new AnnotationDefList();
WaitForCondition(3 * 1000, () => Settings.Default.AnnotationDefList.Count == 0);
RunDlg <MessageDlg>(() => SkylineWindow.RunTool(4), dlg =>
{
Assert.AreEqual(TextUtil.LineSeparate(Resources.ToolDescription_VerifyAnnotations_This_tool_requires_the_use_of_the_following_annotations_which_are_missing_or_improperly_formatted,
string.Empty,
TextUtil.LineSeparate(new Collection <string> {
sampleId.GetKey()
}),
string.Empty,
Resources.ToolDescription_VerifyAnnotations_Please_re_install_the_tool_and_try_again_), dlg.Message);
dlg.OkDialog();
});
// Clean-up
RunDlg <ConfigureToolsDlg>(() => SkylineWindow.ShowConfigureToolsDlg(), dlg =>
{
dlg.RemoveAllTools();
dlg.OkDialog();
});
}
private void ZipTestAnnotations()
{
var sampleId = new AnnotationDef("SampleID", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.replicate),
AnnotationDef.AnnotationType.text,
new List<string>());
var isConc = new AnnotationDef("IS Conc", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.replicate),
AnnotationDef.AnnotationType.text,
new List<string>());
var analyteConcentration = new AnnotationDef("Analyte Concentration", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.replicate),
AnnotationDef.AnnotationType.text,
new List<string>());
var sampleIdTransition = new AnnotationDef("SampleID", // Not L10N
AnnotationDef.AnnotationTargetSet.Singleton(
AnnotationDef.AnnotationTarget.transition),
AnnotationDef.AnnotationType.text,
new List<string>());
// Test proper loading of annotations
string testAnnotationsPath = TestFilesDir.GetTestPath("TestAnnotations.zip"); // Not L10N
RunDlg<ConfigureToolsDlg>(() => SkylineWindow.ShowConfigureToolsDlg(), dlg =>
{
dlg.RemoveAllTools();
dlg.InstallZipTool(testAnnotationsPath);
WaitForConditionUI(3 * 1000, () => dlg.ToolList.Count == 4);
ToolDescription t0 = dlg.ToolList[0];
ToolDescription t1 = dlg.ToolList[1];
ToolDescription t2 = dlg.ToolList[2];
ToolDescription t3 = dlg.ToolList[3];
AssertEx.AreEqualDeep(t0.Annotations, new List<AnnotationDef>());
AssertEx.AreEqualDeep(t1.Annotations,
new List<AnnotationDef>
{
sampleId,
isConc,
analyteConcentration
});
AssertEx.AreEqualDeep(t2.Annotations, new List<AnnotationDef> { sampleId });
AssertEx.AreEqualDeep(t3.Annotations, new List<AnnotationDef>());
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(sampleId));
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(isConc));
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(analyteConcentration));
dlg.OkDialog();
});
// Test conflicting annotations
var configureToolsDlg = ShowDialog<ConfigureToolsDlg>(SkylineWindow.ShowConfigureToolsDlg);
string conflictAnnotationsPath = TestFilesDir.GetTestPath("ConflictAnnotations.zip"); // Not L10N
RunDlg<MultiButtonMsgDlg>(() => configureToolsDlg.InstallZipTool(conflictAnnotationsPath),
messageDlg => messageDlg.Btn1Click()); // keep existing annotations
WaitForConditionUI(3 * 1000, () => configureToolsDlg.ToolList.Count == 5);
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(sampleId));
RunDlg<MultiButtonMsgDlg>(() => configureToolsDlg.InstallZipTool(conflictAnnotationsPath),
dlg => dlg.Btn0Click());
{
var messageDlg = WaitForOpenForm<MultiButtonMsgDlg>();
OkDialog(messageDlg, messageDlg.Btn0Click);
}
// overwrite existing annotations
Assert.IsTrue(Settings.Default.AnnotationDefList.Contains(sampleIdTransition));
OkDialog(configureToolsDlg, configureToolsDlg.OkDialog);
RunUI(() => SkylineWindow.PopulateToolsMenu());
// Test running the tool with an unchecked annotation
RunDlg<MessageDlg>(() => SkylineWindow.RunTool(4), dlg =>
{
Assert.AreEqual(TextUtil.LineSeparate(Resources.ToolDescription_VerifyAnnotations_This_tool_requires_the_use_of_the_following_annotations_which_are_not_enabled_for_this_document,
string.Empty,
TextUtil.LineSeparate(new Collection<string> {sampleId.GetKey()}),
string.Empty,
Resources.ToolDescription_VerifyAnnotations_Please_enable_these_annotations_and_fill_in_the_appropriate_data_in_order_to_use_the_tool_), dlg.Message);
dlg.OkDialog();
});
// Test running the tool with a missing annotation
Settings.Default.AnnotationDefList = new AnnotationDefList();
WaitForCondition(3*1000, () => Settings.Default.AnnotationDefList.Count == 0);
RunDlg<MessageDlg>(() => SkylineWindow.RunTool(4), dlg =>
{
Assert.AreEqual(TextUtil.LineSeparate(Resources.ToolDescription_VerifyAnnotations_This_tool_requires_the_use_of_the_following_annotations_which_are_missing_or_improperly_formatted,
string.Empty,
TextUtil.LineSeparate(new Collection<string> { sampleId.GetKey() }),
string.Empty,
Resources.ToolDescription_VerifyAnnotations_Please_re_install_the_tool_and_try_again_), dlg.Message);
dlg.OkDialog();
});
// Clean-up
RunDlg<ConfigureToolsDlg>(() => SkylineWindow.ShowConfigureToolsDlg(), dlg =>
{
dlg.RemoveAllTools();
dlg.OkDialog();
});
}
