public void CompareAveragingWithMSstats()
{
var srmDocument = LoadRatPlasmaDocument();
var documentContainer = new MemoryDocumentContainer();
documentContainer.SetDocument(documentContainer.Document, srmDocument);
GroupComparisonModel model = new GroupComparisonModel(documentContainer, null);
model.GroupComparisonDef = GroupComparisonDef.EMPTY.ChangeControlAnnotation("Condition")
.ChangeControlValue("Healthy")
.ChangeIdentityAnnotation("BioReplicate")
.ChangeSummarizationMethod(SummarizationMethod.AVERAGING)
.ChangePerProtein(false);
var expectedValues = MsStatsTestUtil.ReadExpectedResults(typeof (MSstatsAveragingTest),
"RatPlasmaTestingResult.csv");
var groupComparer = new GroupComparer(model.GroupComparisonDef, srmDocument, new QrFactorizationCache());
foreach (var protein in srmDocument.PeptideGroups)
{
foreach (var peptide in protein.Peptides)
{
var result = groupComparer.CalculateFoldChange(new GroupComparisonSelector(protein, peptide, IsotopeLabelType.light, null, new GroupIdentifier("Diseased")), null);
var expectedResult = expectedValues[peptide.Peptide.Sequence];
Assert.AreEqual(expectedResult.EstimatedValue, result.LinearFitResult.EstimatedValue,
(expectedResult.StandardError + result.LinearFitResult.StandardError) * 2, peptide.Peptide.Sequence);
}
}
}
public CheckReportCompatibility(SrmDocument document)
{
IDocumentContainer documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(document, null));
_database = new Database(document.Settings);
_database.AddSrmDocument(document);
_dataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
}
private string GetReportRows(SrmDocument document, ViewSpec viewSpec, IProgressMonitor progressMonitor)
{
var container = new MemoryDocumentContainer();
container.SetDocument(document, container.Document);
var dataSchema = new SkylineDataSchema(container, DataSchemaLocalizer.INVARIANT);
var viewContext = new DocumentGridViewContext(dataSchema);
IProgressStatus status = new ProgressStatus(string.Format(Resources.ReportSpec_ReportToCsvString_Exporting__0__report,
viewSpec.Name));
var writer = new StringWriter();
if (viewContext.Export(CancellationToken.None, progressMonitor, ref status, viewContext.GetViewInfo(null, viewSpec), writer,
viewContext.GetCsvWriter()))
{
return(writer.ToString());
}
return(null);
}
private string GetReportRows(SrmDocument document, ViewSpec viewSpec, IProgressMonitor progressMonitor)
{
var container = new MemoryDocumentContainer();
container.SetDocument(document, container.Document);
var dataSchema = new SkylineDataSchema(container, DataSchemaLocalizer.INVARIANT);
var viewContext = new DocumentGridViewContext(dataSchema);
var status = new ProgressStatus(string.Format(Resources.ReportSpec_ReportToCsvString_Exporting__0__report,
viewSpec.Name));
var writer = new StringWriter();
if (viewContext.Export(progressMonitor, ref status, viewContext.GetViewInfo(null, viewSpec), writer,
new DsvWriter(CultureInfo.InvariantCulture, TextUtil.SEPARATOR_CSV)))
{
return writer.ToString();
}
return null;
}
public void TestMapping()
{
var settings = SrmSettingsList.GetDefault();
var document = new SrmDocument(settings);
var documentContainer = new MemoryDocumentContainer();
documentContainer.SetDocument(document, null);
using (var database = new Database(settings))
{
var dataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
var sessionFactory = database.SessionFactory;
foreach (var classMetaData in sessionFactory.GetAllClassMetadata().Values)
{
var tableType = classMetaData.GetMappedClass(EntityMode.Poco);
foreach (var propertyName in classMetaData.PropertyNames)
{
if (propertyName == "Protein" && tableType == typeof (DbProteinResult))
{
continue;
}
var queryDef = new QueryDef
{
Select = new[] {new ReportColumn(tableType, propertyName),}
};
var reportSpec = new ReportSpec("test", queryDef);
var newTableType = ReportSpecConverter.GetNewTableType(reportSpec);
Assert.IsNotNull(newTableType, "No table for type {0}", tableType);
var converter = new ReportSpecConverter(dataSchema);
var viewInfo = converter.Convert(reportSpec);
Assert.IsNotNull(viewInfo, "Unable to convert property {0} in table {1}", propertyName, tableType);
Assert.AreEqual(1, viewInfo.DisplayColumns.Count, "No conversion for property {0} in table {1}", propertyName, tableType);
Assert.IsNotNull(viewInfo.DisplayColumns[0].ColumnDescriptor, "Column not found for property {0} in table {1}", propertyName, tableType);
var report = Report.Load(reportSpec);
var resultSet = report.Execute(database);
var bindingListSource = new BindingListSource();
bindingListSource.SetViewContext(new SkylineViewContext(viewInfo.ParentColumn, Array.CreateInstance(viewInfo.ParentColumn.PropertyType, 0)), viewInfo);
var properties = bindingListSource.GetItemProperties(null);
var oldCaptions = resultSet.ColumnInfos.Select(columnInfo => columnInfo.Caption).ToArray();
var newCaptions = properties.Cast<PropertyDescriptor>().Select(pd=>pd.DisplayName).ToArray();
if (oldCaptions.Length != newCaptions.Length)
{
Console.Out.WriteLine(oldCaptions);
}
CollectionAssert.AreEqual(oldCaptions, newCaptions, "Caption mismatch on {0} in {1}", propertyName, tableType);
for (int i = 0; i < resultSet.ColumnInfos.Count; i++)
{
var columnInfo = resultSet.ColumnInfos[i];
var formatAttribute = (FormatAttribute)properties[i].Attributes[typeof(FormatAttribute)];
string message = string.Format("Format problem on column converted from {0} in {1}",
columnInfo.ReportColumn.Column, columnInfo.ReportColumn.Table);
if (null == columnInfo.Format)
{
Assert.IsTrue(null == formatAttribute || null == formatAttribute.Format, message);
}
else
{
Assert.IsNotNull(formatAttribute, message);
Assert.AreEqual(columnInfo.Format, formatAttribute.Format, message);
}
if (columnInfo.IsNumeric)
{
Assert.IsNotNull(formatAttribute, message);
Assert.AreEqual(TextUtil.EXCEL_NA, formatAttribute.NullValue, message);
}
else
{
Assert.IsTrue(null == formatAttribute || null == formatAttribute.NullValue, message);
}
}
}
}
}
}
public void TestPivotResultsThenIsotopeLabel()
{
var assembly = typeof (LiveReportPivotTest).Assembly;
XmlSerializer documentSerializer = new XmlSerializer(typeof(SrmDocument));
// ReSharper disable once AssignNullToNotNullAttribute
var document = (SrmDocument)documentSerializer.Deserialize(
assembly.GetManifestResourceStream(typeof(ReportSpecConverterTest), "silac_1_to_4.sky"));
XmlSerializer reportSerializer = new XmlSerializer(typeof(ReportOrViewSpecList));
// ReSharper disable once AssignNullToNotNullAttribute
var views = (ReportOrViewSpecList) reportSerializer.Deserialize(
assembly.GetManifestResourceStream(typeof(ReportSpecConverterTest), "LiveReportPivots.skyr"));
var view = views.First(reportSpec => reportSpec.Name == "ResultSummaryPivotResultsThenLabelType").ViewSpec;
var bindingListSource = new BindingListSource();
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(document, null));
var dataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
bindingListSource.SetViewContext(new DocumentGridViewContext(dataSchema), new ViewInfo(dataSchema, typeof(Precursor), view));
var expectedColumnNames = new[] {
"PeptideSequence",
"Chromatograms Replicate",
"Chromatograms PeptideRetentionTime",
"light IsotopeLabelType",
"light MeanTotalArea",
"light Chromatograms TotalArea",
"heavy IsotopeLabelType",
"heavy MeanTotalArea",
"heavy Chromatograms TotalArea",
};
var actualColumnNames =
bindingListSource.GetItemProperties(null)
.Cast<PropertyDescriptor>()
.Select(pd => pd.DisplayName)
.ToArray();
CollectionAssert.AreEqual(expectedColumnNames, actualColumnNames);
}
public void ConsoleReportExportTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
string outPath = testFilesDir.GetTestPath("Exported_test_report.csv");
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("ah_20101011y_BSA_MS-MS_only_5-2" +
ExtensionTestContext.ExtThermoRaw);
const string replicate = "Single";
//Before generating this report, check that it exists
string reportName = Resources.ReportSpecList_GetDefaults_Peptide_Ratio_Results;
Settings.Default.PersistedViews.ResetDefaults();
Assert.IsNotNull(Settings.Default.PersistedViews.GetViewSpecList(PersistedViews.MainGroup.Id)
.GetView(Resources.ReportSpecList_GetDefaults_Peptide_Ratio_Results));
//First, programmatically generate the report
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
//Attach replicate
ProgressStatus status;
doc = CommandLine.ImportResults(doc, docPath, replicate, MsDataFileUri.Parse(rawPath), null, null, out status);
Assert.IsNull(status);
string programmaticReport;
MemoryDocumentContainer memoryDocumentContainer = new MemoryDocumentContainer();
Assert.IsTrue(memoryDocumentContainer.SetDocument(doc, memoryDocumentContainer.Document));
SkylineDataSchema skylineDataSchema = new SkylineDataSchema(memoryDocumentContainer, SkylineDataSchema.GetLocalizedSchemaLocalizer());
DocumentGridViewContext viewContext = new DocumentGridViewContext(skylineDataSchema);
ViewInfo viewInfo = viewContext.GetViewInfo(PersistedViews.MainGroup.Id.ViewName(reportName));
StringWriter writer = new StringWriter();
status = new ProgressStatus("Exporting report");
viewContext.Export(null, ref status, viewInfo, writer,
new DsvWriter(CultureInfo.CurrentCulture, TextUtil.GetCsvSeparator(LocalizationHelper.CurrentCulture)));
programmaticReport = writer.ToString();
RunCommand("--in=" + docPath,
"--import-file=" + rawPath,
"--import-replicate-name=" + replicate,
"--report-name=" + reportName,
"--report-format=CSV",
"--report-file=" + outPath);
string reportLines = File.ReadAllText(outPath);
AssertEx.NoDiff(reportLines, programmaticReport);
}
private SkylineDataSchema GetDataSchema()
{
var document = new SrmDocument(SrmSettingsList.GetDefault());
var container = new MemoryDocumentContainer();
Assert.IsTrue(container.SetDocument(document, container.Document));
return new SkylineDataSchema(container, DataSchemaLocalizer.INVARIANT);
}
public void TestGenerateResxFile()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
GenerateResXFile(new StringWriter() /* Console.Out */, new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT), STARTING_TYPES);
}
public void TestCheckForUnusedColumnCaptions()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
SkylineDataSchema dataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
var columnCaptions = new HashSet<string>();
foreach (
var resourceManager in SkylineDataSchema.GetLocalizedSchemaLocalizer().ColumnCaptionResourceManagers)
{
var resourceSet = resourceManager.GetResourceSet(CultureInfo.InvariantCulture, true, true);
var enumerator = resourceSet.GetEnumerator();
while (enumerator.MoveNext())
{
string key = enumerator.Key as string;
if (null != key)
{
columnCaptions.Add(key);
}
}
}
foreach (var columnDescriptor in EnumerateAllColumnDescriptors(dataSchema, STARTING_TYPES)
)
{
var invariantCaption = dataSchema.GetColumnCaption(columnDescriptor);
columnCaptions.Remove(invariantCaption.InvariantCaption);
}
var unusedCaptions = columnCaptions.ToArray();
Assert.AreEqual(0, unusedCaptions.Length, "Unused entries found in ColumnCaptions.resx: {0}", string.Join(",", unusedCaptions));
}
public void TestAllColumnCaptionsAreLocalized()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
SkylineDataSchema skylineDataSchema = new SkylineDataSchema(documentContainer, SkylineDataSchema.GetLocalizedSchemaLocalizer());
var missingCaptions = new HashSet<ColumnCaption>();
foreach (var columnDescriptor in
EnumerateAllColumnDescriptors(skylineDataSchema, STARTING_TYPES))
{
var invariantCaption = skylineDataSchema.GetColumnCaption(columnDescriptor);
if (!skylineDataSchema.DataSchemaLocalizer.HasEntry(invariantCaption))
{
missingCaptions.Add(invariantCaption);
}
}
if (missingCaptions.Count == 0)
{
return;
}
StringWriter message = new StringWriter();
WriteResXFile(message, missingCaptions);
Assert.Fail("Missing localized column captions {0}", message);
}
private MemoryDocumentContainer CreateMemoryDocumentContainer(SrmDocument document)
{
MemoryDocumentContainer memoryDocumentContainer = new MemoryDocumentContainer();
Assert.IsTrue(memoryDocumentContainer.SetDocument(document, memoryDocumentContainer.Document));
return memoryDocumentContainer;
}
