public void TestCommandLineImportAnnotations()
{
var testFilesDir = new TestFilesDir(TestContext, @"TestA\CommandLineImportAnnotationsTest.zip");
var inDocPath = testFilesDir.GetTestPath("original.sky");
var outDocPath = testFilesDir.GetTestPath("AnnotatedDocument.sky");
var annotationPath = testFilesDir.GetTestPath("annotations.csv");
SrmDocument originalDocument;
using (var stream = new FileStream(inDocPath, FileMode.Open))
{
originalDocument = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(stream);
}
Assert.IsTrue(originalDocument.Settings.HasResults);
var replicateAnnotation =
originalDocument.Settings.DataSettings.AnnotationDefs.First(
def => def.Name == REPLICATE_ANNOTATION);
Assert.IsNotNull(replicateAnnotation);
Assert.IsTrue(replicateAnnotation.AnnotationTargets.Contains(AnnotationDef.AnnotationTarget.replicate));
Assert.AreEqual(AnnotationDef.AnnotationType.text, replicateAnnotation.Type);
var chromatograms = originalDocument.MeasuredResults.Chromatograms.ToArray();
Assert.AreNotEqual(0, chromatograms.Length);
for (int i = 0; i < chromatograms.Length; i++)
{
var chromSet = chromatograms[i];
chromSet = chromSet.ChangeAnnotations(
chromSet.Annotations.ChangeAnnotation(replicateAnnotation, "Replicate" + i));
chromatograms[i] = chromSet;
}
SrmDocument annotatedDocument = originalDocument.ChangeMeasuredResults(
originalDocument.MeasuredResults.ChangeChromatograms(chromatograms));
Assert.AreNotEqual(originalDocument, annotatedDocument);
var documentAnnotations = new DocumentAnnotations(annotatedDocument);
documentAnnotations.WriteAnnotationsToFile(CancellationToken.None, ExportAnnotationSettings.AllAnnotations(annotatedDocument), annotationPath);
Assert.IsTrue(File.Exists(annotationPath));
RunCommand("--in=" + inDocPath, "--out=" + outDocPath, "--import-annotations=" + annotationPath);
Assert.IsTrue(File.Exists(outDocPath));
SrmDocument outputDocument;
using (var stream = new FileStream(outDocPath, FileMode.Open))
{
outputDocument = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(stream);
}
Assert.AreEqual(annotatedDocument.Settings.MeasuredResults.Chromatograms,
outputDocument.Settings.MeasuredResults.Chromatograms);
}
protected override void DoTest()
{
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("ImportAnnotationsTest.sky")));
WaitForDocumentLoaded();
var annotationAdder = new AnnotationAdder();
Assert.IsTrue(SkylineWindow.SetDocument(annotationAdder.DefineTestAnnotations(SkylineWindow.Document), SkylineWindow.Document));
var annotatedDocument = annotationAdder.AddAnnotationTestValues(SkylineWindow.Document);
var annotationSettings = ExportAnnotationSettings.AllAnnotations(annotatedDocument)
.ChangeRemoveBlankRows(true);
var documentAnnotations = new DocumentAnnotations(annotatedDocument);
string annotationPath = TestFilesDir.GetTestPath("annotations.csv");
documentAnnotations.WriteAnnotationsToFile(CancellationToken.None, annotationSettings, annotationPath);
RunUI(() => SkylineWindow.ImportAnnotations(annotationPath));
Assert.AreEqual(annotatedDocument, SkylineWindow.Document);
using (var reader = new StreamReader(annotationPath))
{
var lines = reader.ReadToEnd().Split('\n').Where(line => !string.IsNullOrEmpty(line)).ToArray();
Assert.AreEqual(annotationAdder.ElementCount + 1, lines.Length);
}
}
