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 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);
}