public static Type GetRootTable(ReportSpec reportSpec)
{
var types = reportSpec.Select.Select(GetRootTable).Distinct().ToArray();
if (types.Length == 1)
{
return(types[0]);
}
return(null);
}
public override void WriteXml(XmlWriter writer)
{
if (ViewSpec != null)
{
ViewSpec.WriteXml(writer);
}
else
{
ReportSpec.WriteXml(writer);
}
}
public override void ReadXml(XmlReader reader)
{
base.ReadXml(reader);
if (null != reader.GetAttribute("rowsource") || null != reader.GetAttribute("sublist")) // Not L10N
{
ViewSpec = ViewSpec.ReadXml(reader);
}
else
{
ReportSpec = ReportSpec.Deserialize(reader);
}
}
public new ReportOrViewSpec ChangeName(string newName)
{
if (null != ViewSpec)
{
return(new ReportOrViewSpec(ViewSpec.SetName(newName)));
}
if (null != ReportSpec)
{
return(new ReportOrViewSpec((ReportSpec)ReportSpec.ChangeName(newName)));
}
return((ReportOrViewSpec)base.ChangeName(newName));
}
public override void ReadXml(XmlReader reader)
{
base.ReadXml(reader);
if (null != reader.GetAttribute(@"rowsource") || null != reader.GetAttribute(@"sublist"))
{
ViewSpecLayout = new ViewSpecLayout(ViewSpec.ReadXml(reader), ViewLayoutList.EMPTY);
}
else
{
ReportSpec = ReportSpec.Deserialize(reader);
}
}
private bool TryGetReport(SrmDocument document, ReportSpec reportSpec, out string report)
{
lock (_cacheLock)
{
if (ReferenceEquals(document, _document) && _dictionary.TryGetValue(reportSpec, out report))
{
_list.Remove(reportSpec);
_list.AddFirst(reportSpec);
return(true);
}
}
report = null;
return(false);
}
public new ReportOrViewSpec ChangeName(string newName)
{
if (null != ViewSpecLayout)
{
return(new ReportOrViewSpec(ViewSpecLayout.ChangeName(newName)));
}
if (null != ReportSpec)
{
return(new ReportOrViewSpec((ReportSpec)ReportSpec.ChangeName(newName)));
}
throw new InvalidOperationException();
}
public void SetReportSpec(ReportSpec reportSpec)
{
if (reportSpec == null)
{
textName.Text = string.Empty;
SetReport(new SimpleReport());
}
else
{
textName.Text = reportSpec.Name;
SetReport(Report.Load(reportSpec));
}
_reportSpec = reportSpec;
}
public static void ReportToCsv(ReportSpec reportSpec, SrmDocument doc, string fileName, CultureInfo cultureInfo)
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(doc, documentContainer.Document));
var skylineDataSchema = new SkylineDataSchema(documentContainer, new DataSchemaLocalizer(cultureInfo, cultureInfo));
var viewSpec = ReportSharing.ConvertAll(new[] { new ReportOrViewSpec(reportSpec) }, doc).First();
var viewContext = new DocumentGridViewContext(skylineDataSchema);
using (var writer = new StreamWriter(fileName))
{
IProgressStatus status = new ProgressStatus();
viewContext.Export(CancellationToken.None, new SilentProgressMonitor(), ref status,
viewContext.GetViewInfo(ViewGroup.BUILT_IN, viewSpec), writer, viewContext.GetCsvWriter());
}
}
public void ReportToCsv(ReportSpec reportSpec, SrmDocument doc, string fileName, CultureInfo cultureInfo)
{
Report report = Report.Load(reportSpec);
using (var saver = new FileSaver(fileName))
using (var writer = new StreamWriter(saver.SafeName))
using (var database = new Database(doc.Settings))
{
database.AddSrmDocument(doc);
var resultSet = report.Execute(database);
char separator = TextUtil.GetCsvSeparator(cultureInfo);
ResultSet.WriteReportHelper(resultSet, separator, writer, cultureInfo);
writer.Flush();
writer.Close();
saver.Commit();
}
}
public void ReportToCsv(ReportSpec reportSpec, SrmDocument doc, string fileName)
{
Report report = Report.Load(reportSpec);
using (var saver = new FileSaver(fileName))
using (var writer = new StreamWriter(saver.SafeName))
using (var database = new Database(doc.Settings))
{
database.AddSrmDocument(doc);
var resultSet = report.Execute(database);
char separator = TextUtil.CsvSeparator;
ResultSet.WriteReportHelper(resultSet, separator, writer, LocalizationHelper.CurrentCulture);
writer.Flush();
writer.Close();
saver.Commit();
}
}
/// <summary>
/// Returns the .csv file generated by exporting the given ReportSpec using data from the given Document.
/// </summary>
/// <param name="document">The current document open in Skyline</param>
/// <param name="reportSpec">The export report format</param>
/// <param name="progressMonitor"></param>
public string GetReport(SrmDocument document, ReportSpec reportSpec, IProgressMonitor progressMonitor)
{
string report;
if (TryGetReport(document, reportSpec, out report))
{
return(report);
}
// Only on report at a time can be generated
lock (_reportGenLock)
{
// Try again, in case we were waiting for the report we want to be generated
if (TryGetReport(document, reportSpec, out report))
{
return(report);
}
report = TestReport ?? reportSpec.ReportToCsvString(document, progressMonitor);
lock (_cacheLock)
{
// if the document has changed while the report was exporting, don't add it to the cache
if (ReferenceEquals(document, _document))
{
CurrentSize += ReportSize(report);
while (CurrentSize > (TestMaximumSize ?? MAXIMUM_SIZE))
{
// remove the oldest reports
ReportSpec oldestSpec = _list.Last.Value;
string oldestReport;
if (_dictionary.TryGetValue(oldestSpec, out oldestReport))
{
_dictionary.Remove(oldestSpec);
CurrentSize -= ReportSize(oldestReport);
}
_list.RemoveLast();
}
_list.AddFirst(reportSpec);
_dictionary.Add(reportSpec, report);
}
}
return(report);
}
}
public static Report Load(ReportSpec reportSpec)
{
SimpleReport simpleReport;
if (reportSpec.CrossTabHeaders != null)
{
PivotReport pivotReport = new PivotReport
{
GroupByColumns = reportSpec.GroupBy,
CrossTabHeaders = reportSpec.CrossTabHeaders,
CrossTabValues = reportSpec.CrossTabValues
};
simpleReport = pivotReport;
}
else
{
simpleReport = new SimpleReport();
}
simpleReport.Columns = reportSpec.Select;
return simpleReport;
}
public static Type GetNewTableType(ReportSpec reportSpec)
{
var rowTypes = new List <Type>();
foreach (var column in reportSpec.Select)
{
var rowType = GetRootTable(column);
if (null != rowType)
{
rowTypes.Add(rowType);
}
}
var unique = rowTypes.Distinct().ToArray();
if (unique.Length != 1)
{
return(null);
}
return(unique[0]);
}
public static Report Load(ReportSpec reportSpec)
{
SimpleReport simpleReport;
if (reportSpec.CrossTabHeaders != null)
{
PivotReport pivotReport = new PivotReport
{
GroupByColumns = reportSpec.GroupBy,
CrossTabHeaders = reportSpec.CrossTabHeaders,
CrossTabValues = reportSpec.CrossTabValues
};
simpleReport = pivotReport;
}
else
{
simpleReport = new SimpleReport();
}
simpleReport.Columns = reportSpec.Select;
return(simpleReport);
}
/// <summary>
/// In old custom reports, if the report was showing rows from a Results table,
/// the report would not include any DocNode's which did not have any results.
/// To preserve this behavior we add a filter that only DocNode's which have at
/// least one Result get included.
/// </summary>
public static ViewSpec AddFilter(ViewSpec viewSpec, ReportSpec reportSpec)
{
var propertyPaths = new HashSet<PropertyPath>();
IEnumerable<ReportColumn> columns = reportSpec.Select;
if (reportSpec.CrossTabValues != null)
{
columns = columns.Concat(reportSpec.CrossTabValues);
}
foreach (var reportColumn in columns)
{
var databindingTableAttribute = GetDatabindingTableAttribute(reportColumn);
if (null != databindingTableAttribute.Property && !databindingTableAttribute.Property.EndsWith("Summary")) // Not L10N
{
propertyPaths.Add(PropertyPath.Parse(databindingTableAttribute.Property));
}
}
var newFilters =
propertyPaths.Select(
propertyPath => new FilterSpec(propertyPath, FilterOperations.OP_IS_NOT_BLANK, null));
viewSpec = viewSpec.SetFilters(viewSpec.Filters.Concat(newFilters));
return viewSpec;
}
/// <summary>
/// In old custom reports, if the report was showing rows from a Results table,
/// the report would not include any DocNode's which did not have any results.
/// To preserve this behavior we add a filter that only DocNode's which have at
/// least one Result get included.
/// </summary>
public static ViewSpec AddFilter(ViewSpec viewSpec, ReportSpec reportSpec)
{
var propertyPaths = new HashSet <PropertyPath>();
IEnumerable <ReportColumn> columns = reportSpec.Select;
if (reportSpec.CrossTabValues != null)
{
columns = columns.Concat(reportSpec.CrossTabValues);
}
foreach (var reportColumn in columns)
{
var databindingTableAttribute = GetDatabindingTableAttribute(reportColumn);
if (null != databindingTableAttribute.Property && !databindingTableAttribute.Property.EndsWith(@"Summary"))
{
propertyPaths.Add(PropertyPath.Parse(databindingTableAttribute.Property));
}
}
var newFilters = propertyPaths.Select(propertyPath => new FilterSpec(propertyPath, FilterPredicate.IS_NOT_BLANK));
viewSpec = viewSpec.SetFilters(viewSpec.Filters.Concat(newFilters));
return(viewSpec);
}
public void CheckReport(ReportSpec reportSpec)
{
string message = string.Format("Report {0}", reportSpec.Name);
var converter = new ReportSpecConverter(_dataSchema);
var viewInfo = converter.Convert(reportSpec);
var report = Report.Load(reportSpec);
ResultSet resultSet;
try
{
resultSet = report.Execute(_database);
}
catch (Exception)
{
return;
}
using (var bindingListSource = new BindingListSource())
{
bindingListSource.SetViewContext(new SkylineViewContext(viewInfo.ParentColumn, GetRowSource(viewInfo)),
viewInfo);
var oldCaptions = resultSet.ColumnInfos.Select(columnInfo => columnInfo.Caption).ToArray();
var properties = bindingListSource.GetItemProperties(null);
IList resultRows = bindingListSource;
var newCaptions = properties.Cast<PropertyDescriptor>().Select(pd => pd.DisplayName).ToArray();
if (!oldCaptions.SequenceEqual(newCaptions))
{
CollectionAssert.AreEqual(oldCaptions, newCaptions, message);
}
if (resultSet.RowCount != resultRows.Count)
{
Assert.AreEqual(resultSet.RowCount, resultRows.Count, message);
}
resultRows = SortRows(resultRows, properties);
resultSet = SortResultSet(resultSet);
for (int iRow = 0; iRow < resultSet.RowCount; iRow++)
{
for (int iCol = 0; iCol < resultSet.ColumnInfos.Count; iCol++)
{
var propertyDescriptor = properties[iCol];
object oldValue = resultSet.GetRow(iRow)[iCol];
object newValue = propertyDescriptor.GetValue(resultRows[iRow]);
if (!Equals(oldValue, newValue))
{
Assert.AreEqual(oldValue, newValue,
message + "{0}:Values are not equal on Row {1} Column {2} ({3}) FullName:{4}",
message, iRow, iCol, propertyDescriptor.DisplayName, propertyDescriptor.Name);
}
}
}
foreach (char separator in new[] { ',', '\t' })
{
StringWriter oldStringWriter = new StringWriter();
var cultureInfo = LocalizationHelper.CurrentCulture;
ResultSet.WriteReportHelper(resultSet, separator, oldStringWriter, cultureInfo);
StringWriter newStringWriter = new StringWriter();
var skylineViewContext = (SkylineViewContext) bindingListSource.ViewContext;
ProgressStatus progressStatus = new ProgressStatus("Status");
skylineViewContext.Export(null, ref progressStatus, viewInfo, newStringWriter,
new DsvWriter(cultureInfo, separator));
var newLineSeparators = new[] { "\r\n" };
var oldLines = oldStringWriter.ToString().Split(newLineSeparators, StringSplitOptions.None);
var newLines = newStringWriter.ToString().Split(newLineSeparators, StringSplitOptions.None);
// TODO(nicksh): Old reports would hide columns for annotations that were not in the document.
bool anyHiddenColumns = resultSet.ColumnInfos.Any(column => column.IsHidden);
if (!anyHiddenColumns)
{
Assert.AreEqual(oldLines[0], newLines[0]);
CollectionAssert.AreEquivalent(oldLines, newLines);
}
}
}
}
/// <summary>
/// Добавление контента, прописанного в базе конфигурации
/// </summary>
protected void AddContentFromBase(UserRights userRights, Dictionary <string, UiObjSpec> uiObjSpecs,
DataAccess dataAccess)
{
if (userRights != null && uiObjSpecs != null)
{
List <UiObjProps> uiObjPropsList = dataAccess.GetUiObjPropsList(
UiObjProps.BaseUiTypes.Report | UiObjProps.BaseUiTypes.DataWnd);
foreach (UiObjProps uiObjProps in uiObjPropsList)
{
int uiObjID = uiObjProps.UiObjID;
if (userRights.GetUiObjRights(uiObjID).ViewRight)
{
UiObjSpec uiObjSpec;
uiObjSpecs.TryGetValue(uiObjProps.TypeCode, out uiObjSpec);
if (uiObjProps.BaseUiType == UiObjProps.BaseUiTypes.Report)
{
// добавление элемента отчёта
ReportItem reportItem = new ReportItem()
{
UiObjID = uiObjID,
Text = uiObjProps.Title,
Path = uiObjProps.Path
};
if (uiObjSpec is ReportSpec)
{
ReportSpec reportSpec = (ReportSpec)uiObjSpec;
if (string.IsNullOrEmpty(reportItem.Text))
{
reportItem.Text = reportSpec.Name;
}
reportItem.Url = uiObjSpec.GetUrl(uiObjID);
reportItem.ReportSpec = reportSpec;
}
if (!string.IsNullOrEmpty(reportItem.Text))
{
ReportItems.Add(reportItem);
reportItemDict[uiObjID] = reportItem;
}
}
else if (uiObjProps.BaseUiType == UiObjProps.BaseUiTypes.DataWnd)
{
// добавление элемента окна данных
DataWndItem dataWndItem = new DataWndItem()
{
UiObjID = uiObjID,
Text = uiObjProps.Title,
Path = uiObjProps.Path
};
if (uiObjSpec is DataWndSpec)
{
DataWndSpec dataWndSpec = (DataWndSpec)uiObjSpec;
if (string.IsNullOrEmpty(dataWndItem.Text))
{
dataWndItem.Text = dataWndSpec.Name;
}
dataWndItem.Url = uiObjSpec.GetUrl(uiObjID);
dataWndItem.DataWndSpec = dataWndSpec;
}
if (!string.IsNullOrEmpty(dataWndItem.Text))
{
DataWndItems.Add(dataWndItem);
dataWndItemDict[uiObjID] = dataWndItem;
}
}
}
}
}
}
public bool ContainsKey(ReportSpec reportSpec)
{
return _dictionary.ContainsKey(reportSpec) && _list.Contains(reportSpec);
}
public void CheckReport(ReportSpec reportSpec)
{
string message = string.Format("Report {0}", reportSpec.Name);
var converter = new ReportSpecConverter(_dataSchema);
var viewInfo = converter.Convert(reportSpec);
var report = Report.Load(reportSpec);
ResultSet resultSet;
try
{
resultSet = report.Execute(_database);
}
catch (Exception)
{
return;
}
using (var bindingListSource = new BindingListSource())
{
bindingListSource.SetViewContext(new SkylineViewContext(viewInfo.ParentColumn, GetRowSource(viewInfo)),
viewInfo);
var oldCaptions = resultSet.ColumnInfos.Select(columnInfo => columnInfo.Caption).ToArray();
var properties = bindingListSource.GetItemProperties(null);
IList resultRows = bindingListSource;
var newCaptions = properties.Cast <PropertyDescriptor>().Select(pd => pd.DisplayName).ToArray();
if (!oldCaptions.SequenceEqual(newCaptions))
{
CollectionAssert.AreEqual(oldCaptions, newCaptions, message);
}
if (resultSet.RowCount != resultRows.Count)
{
Assert.AreEqual(resultSet.RowCount, resultRows.Count, message);
}
resultRows = SortRows(resultRows, properties);
resultSet = SortResultSet(resultSet);
for (int iRow = 0; iRow < resultSet.RowCount; iRow++)
{
for (int iCol = 0; iCol < resultSet.ColumnInfos.Count; iCol++)
{
var propertyDescriptor = properties[iCol];
object oldValue = resultSet.GetRow(iRow)[iCol];
object newValue = propertyDescriptor.GetValue(resultRows[iRow]);
if (!Equals(oldValue, newValue))
{
Assert.AreEqual(oldValue, newValue,
message + "{0}:Values are not equal on Row {1} Column {2} ({3}) FullName:{4}",
message, iRow, iCol, propertyDescriptor.DisplayName, propertyDescriptor.Name);
}
}
}
foreach (char separator in new[] { ',', '\t' })
{
StringWriter oldStringWriter = new StringWriter();
var cultureInfo = LocalizationHelper.CurrentCulture;
ResultSet.WriteReportHelper(resultSet, separator, oldStringWriter, cultureInfo);
StringWriter newStringWriter = new StringWriter();
var skylineViewContext = (SkylineViewContext)bindingListSource.ViewContext;
ProgressStatus progressStatus = new ProgressStatus("Status");
skylineViewContext.Export(null, ref progressStatus, viewInfo, newStringWriter,
new DsvWriter(cultureInfo, separator));
var newLineSeparators = new[] { "\r\n" };
var oldLines = oldStringWriter.ToString().Split(newLineSeparators, StringSplitOptions.None);
var newLines = newStringWriter.ToString().Split(newLineSeparators, StringSplitOptions.None);
// TODO(nicksh): Old reports would hide columns for annotations that were not in the document.
bool anyHiddenColumns = resultSet.ColumnInfos.Any(column => column.IsHidden);
if (!anyHiddenColumns)
{
Assert.AreEqual(oldLines[0], newLines[0]);
CollectionAssert.AreEquivalent(oldLines, newLines);
}
}
}
}
public void TestImportPeakBoundary()
{
// Load the SRM document and relevant files
var testFilesDir = new TestFilesDir(TestContext, TEST_ZIP_PATH);
bool isIntl = (TextUtil.CsvSeparator != TextUtil.SEPARATOR_CSV);
var precursorMzs = isIntl ? _precursorMzsIntl : _precursorMzsUs;
var peakBoundaryFileTsv = testFilesDir.GetTestPath(isIntl
? "PeakBoundaryTsvIntl.tsv"
: "PeakBoundaryTsv.tsv");
var peakBoundaryFileCsv = testFilesDir.GetTestPath(isIntl
? "PeakBoundaryIntl.csv"
: "PeakBoundaryUS.csv");
var peakBoundaryDoc = testFilesDir.GetTestPath("Chrom05.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(peakBoundaryDoc);
var cult = LocalizationHelper.CurrentCulture;
var cultI = CultureInfo.InvariantCulture;
string csvSep = TextUtil.CsvSeparator.ToString(cultI);
string spaceSep = TextUtil.SEPARATOR_SPACE.ToString(cultI);
// Load an empty doc, so that we can make a change and
// cause the .skyd to be loaded
using (var docContainer = new ResultsTestDocumentContainer(null, peakBoundaryDoc))
{
docContainer.SetDocument(doc, null, true);
docContainer.AssertComplete();
SrmDocument docResults = docContainer.Document;
// Test Tsv import, looking at first .raw file
DoFileImportTests(docResults, peakBoundaryFileTsv, _precursorCharge,
_tsvMinTime1, _tsvMaxTime1, _tsvIdentified1, _tsvAreas1, _peptides, 0, precursorMzs, annote);
// Test Tsv import, looking at second .raw file
DoFileImportTests(docResults, peakBoundaryFileTsv, _precursorCharge,
_tsvMinTime2, _tsvMaxTime2, _tsvIdentified2, _tsvAreas2, _peptides, 1, precursorMzs, annote);
// Test Csv import for local format
DoFileImportTests(docResults, peakBoundaryFileCsv, _precursorCharge,
_csvMinTime1, _csvMaxTime1, _csvIdentified1, _csvAreas1, _peptides, 0, precursorMzs, annote);
DoFileImportTests(docResults, peakBoundaryFileCsv, _precursorCharge,
_csvMinTime2, _csvMaxTime2, _csvIdentified2, _csvAreas2, _peptides, 1, precursorMzs, annote);
// Test that importing same file twice leads to no change to document the second time
var docNew = ImportFileToDoc(docResults, peakBoundaryFileTsv);
var docNewSame = ImportFileToDoc(docNew, peakBoundaryFileTsv);
Assert.AreSame(docNew, docNewSame);
Assert.AreNotSame(docNew, docResults);
// Test that exporting peak boundaries and then importing them leads to no change
string peakBoundaryExport = testFilesDir.GetTestPath("TestRoundTrip.csv");
ReportSpec reportSpec = MakeReportSpec();
ReportToCsv(reportSpec, docNew, peakBoundaryExport);
var docRoundTrip = ImportFileToDoc(docNew, peakBoundaryExport);
Assert.AreSame(docNew, docRoundTrip);
// 1. Empty file -
ImportThrowsException(docResults, string.Empty,
Resources.PeakBoundaryImporter_Import_Failed_to_read_the_first_line_of_the_file);
// 2. No separator in first line
ImportThrowsException(docResults, "No-valid-separators",
TextUtil.CsvSeparator == TextUtil.SEPARATOR_CSV
? Resources.PeakBoundaryImporter_DetermineCorrectSeparator_The_first_line_does_not_contain_any_of_the_possible_separators_comma__tab_or_space_
: Resources.PeakBoundaryImporter_DetermineCorrectSeparator_The_first_line_does_not_contain_any_of_the_possible_separators_semicolon__tab_or_space_);
// 3. Missing field names
ImportThrowsException(docResults, string.Join(csvSep, PeakBoundaryImporter.STANDARD_FIELD_NAMES.Take(3).ToArray()),
Resources.PeakBoundaryImporter_Import_Failed_to_find_the_necessary_headers__0__in_the_first_line);
string headerRow = string.Join(csvSep, PeakBoundaryImporter.STANDARD_FIELD_NAMES.Take(6));
string headerRowSpaced = string.Join(spaceSep, PeakBoundaryImporter.STANDARD_FIELD_NAMES.Take(6));
string[] values =
{
"TPEVDDEALEK", "Q_2012_0918_RJ_13.raw", (3.5).ToString(cult), (4.5).ToString(cult), 2.ToString(cult), 0.ToString(cult)
};
// 4. Mismatched field count
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRow, string.Join(spaceSep, values)),
Resources.PeakBoundaryImporter_Import_Line__0__field_count__1__differs_from_the_first_line__which_has__2_);
// 5. Invalid charge state
string[] valuesBadCharge = new List <string>(values).ToArray();
valuesBadCharge[(int)PeakBoundaryImporter.Field.charge] = (3.5).ToString(cult);
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRow, string.Join(csvSep, valuesBadCharge)),
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_charge_state_);
valuesBadCharge[(int)PeakBoundaryImporter.Field.charge] = TextUtil.EXCEL_NA;
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRow, string.Join(csvSep, valuesBadCharge)),
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_charge_state_);
// 6. Invalid start time
string[] valuesBadTime = new List <string>(values).ToArray();
valuesBadTime[(int)PeakBoundaryImporter.Field.start_time] = "bad";
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)),
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_);
valuesBadTime[(int)PeakBoundaryImporter.Field.end_time] = "bad";
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)),
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_);
// But ok if not adjusting peaks
ImportNoException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)), true, false, false);
// 7. Invalid end time
valuesBadTime[(int)PeakBoundaryImporter.Field.start_time] =
values[(int)PeakBoundaryImporter.Field.start_time];
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)),
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_end_time_);
// But ok if not adjusting peaks
ImportNoException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)), true, false, false);
// #N/A in times ok
valuesBadTime[(int)PeakBoundaryImporter.Field.start_time] =
valuesBadTime[(int)PeakBoundaryImporter.Field.end_time] = TextUtil.EXCEL_NA;
ImportNoException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)));
// If only start time #N/A throws exception
valuesBadTime[(int)PeakBoundaryImporter.Field.start_time] = (3.5).ToString(cult);
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)),
Resources.PeakBoundaryImporter_Import_Missing_end_time_on_line__0_);
// If only end time #N/A throws exception
valuesBadTime[(int)PeakBoundaryImporter.Field.start_time] = TextUtil.EXCEL_NA;
valuesBadTime[(int)PeakBoundaryImporter.Field.end_time] = (3.5).ToString(cult);
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)),
Resources.PeakBoundaryImporter_Import_Missing_start_time_on_line__0_);
// Empty times throws exception
valuesBadTime[(int)PeakBoundaryImporter.Field.start_time] =
valuesBadTime[(int)PeakBoundaryImporter.Field.end_time] = string.Empty;
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadTime)),
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_);
// 8. Not imported file gets skipped
string[] valuesBadFile = new List <string>(values).ToArray();
valuesBadFile[(int)PeakBoundaryImporter.Field.filename] = "Q_2012_0918_RJ_15.raw";
ImportNoException(docResults, TextUtil.LineSeparate(headerRowSpaced, string.Join(spaceSep, valuesBadFile)));
// 9. Unknown modification state gets skipped
string[] valuesBadSequence = new List <string>(values).ToArray();
valuesBadSequence[(int)PeakBoundaryImporter.Field.modified_peptide] = "T[+80]PEVDDEALEK";
ImportNoException(docResults, TextUtil.LineSeparate(headerRow, string.Join(csvSep, valuesBadSequence)));
// 10. Unknown peptide sequence gets skipped
valuesBadSequence[(int)PeakBoundaryImporter.Field.modified_peptide] = "PEPTIDER";
ImportNoException(docResults, TextUtil.LineSeparate(headerRow, string.Join(csvSep, valuesBadSequence)));
// 11. Bad value in decoy field
string[] valuesBadDecoys = new List <string>(values).ToArray();
valuesBadDecoys[(int)PeakBoundaryImporter.Field.is_decoy] = 3.ToString(cult);
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRow, string.Join(csvSep, valuesBadDecoys)),
Resources.PeakBoundaryImporter_Import_The_decoy_value__0__on_line__1__is_invalid__must_be_0_or_1_);
// 12. Import with bad sample throws exception
string[] valuesSample =
{
"TPEVDDEALEK", "Q_2012_0918_RJ_13.raw", (3.5).ToString(cult), (4.5).ToString(cult), 2.ToString(cult), 0.ToString(cult), "badSample"
};
string headerRowSample = string.Join(csvSep, PeakBoundaryImporter.STANDARD_FIELD_NAMES);
ImportThrowsException(docResults, TextUtil.LineSeparate(headerRowSample, string.Join(csvSep, valuesSample)),
Resources.PeakBoundaryImporter_Import_Sample__0__on_line__1__does_not_match_the_file__2__);
// 13. Decoys, charge state, and sample missing ok
var valuesFourFields = valuesSample.Take(4);
string headerFourFields = string.Join(csvSep, PeakBoundaryImporter.STANDARD_FIELD_NAMES.Take(4));
ImportNoException(docResults, TextUtil.LineSeparate(headerFourFields, string.Join(csvSep, valuesFourFields)));
// 14. Valid (charge state, fileName, peptide) combo that is not in document gets skipped
string[] valuesBadCombo = new List <string>(values).ToArray();
valuesBadCombo[(int)PeakBoundaryImporter.Field.charge] = (5).ToString(cult);
ImportNoException(docResults, TextUtil.LineSeparate(headerRow, string.Join(csvSep, valuesBadCombo)));
// Note: Importing with all 7 columns is tested as part of MProphetResultsHandlerTest
}
// Now check a file that has peptide ID's, and see that they're properly ported
var peptideIdPath = testFilesDir.GetTestPath("Template_MS1Filtering_1118_2011_3-2min.sky");
SrmDocument docId = ResultsUtil.DeserializeDocument(peptideIdPath);
docId = docId.ChangeSettings(docId.Settings.ChangePeptideLibraries(libraries =>
{
var lib = libraries.Libraries[0];
return(libraries.ChangeLibrarySpecs(new LibrarySpec[]
{
new BiblioSpecLiteSpec(lib.Name, testFilesDir.GetTestPath(lib.FileNameHint))
}));
}));
using (var docContainerId = new ResultsTestDocumentContainer(null, peptideIdPath))
{
docContainerId.SetDocument(docId, null, true);
docContainerId.AssertComplete();
SrmDocument docResultsId = docContainerId.Document;
var peakBoundaryFileId = testFilesDir.GetTestPath(isIntl
? "Template_MS1Filtering_1118_2011_3-2min_new_intl.tsv"
: "Template_MS1Filtering_1118_2011_3-2min_new.tsv");
DoFileImportTests(docResultsId, peakBoundaryFileId, _precursorChargeId,
_idMinTime1, _idMaxTime1, _idIdentified1, _idAreas1, _peptidesId, 0);
// 15. Decminal import format ok
var headerUnimod = string.Join(csvSep, PeakBoundaryImporter.STANDARD_FIELD_NAMES.Take(4));
var valuesUnimod = new[]
{
"LGGLRPES[+" + string.Format("{0:F01}", 80.0) + "]PESLTSVSR", "100803_0005b_MCF7_TiTip3.wiff", (80.5).ToString(cult), (82.0).ToString(cult)
};
ImportNoException(docResultsId, TextUtil.LineSeparate(headerUnimod, string.Join(csvSep, valuesUnimod)));
// 16. Integer import format ok
valuesUnimod[0] = "LGGLRPES[+80]PESLTSVSR";
ImportNoException(docResultsId, TextUtil.LineSeparate(headerUnimod, string.Join(csvSep, valuesUnimod)));
// 17. Unimod import format ok
valuesUnimod[0] = "LGGLRPES(UniMod:21)PESLTSVSR";
ImportNoException(docResultsId, TextUtil.LineSeparate(headerUnimod, string.Join(csvSep, valuesUnimod)));
// 18. Strange capitalizations OK
valuesUnimod[0] = "LGGLRPES(uniMoD:21)PESLTSVSR";
ImportNoException(docResultsId, TextUtil.LineSeparate(headerUnimod, string.Join(csvSep, valuesUnimod)));
// 18. Unimod with brackets OK
valuesUnimod[0] = "LGGLRPES[uniMoD:21]PESLTSVSR";
ImportNoException(docResultsId, TextUtil.LineSeparate(headerUnimod, string.Join(csvSep, valuesUnimod)));
}
}
public void SetReportSpec(ReportSpec reportSpec)
{
if (reportSpec == null)
{
textName.Text = string.Empty;
SetReport(new SimpleReport());
}
else
{
textName.Text = reportSpec.Name;
SetReport(Report.Load(reportSpec));
}
_reportSpec = reportSpec;
}
public static Type GetRootTable(ReportSpec reportSpec)
{
var types = reportSpec.Select.Select(GetRootTable).Distinct().ToArray();
if (types.Length == 1)
{
return types[0];
}
return null;
}
private void ValidateReport(ReportSpec reportSpec, Type rowType)
{
var dataSchema = GetDataSchema();
var converter = new ReportSpecConverter(dataSchema);
var viewInfo = converter.Convert(reportSpec);
Assert.AreEqual(rowType, viewInfo.ParentColumn.PropertyType);
EnsureViewRoundTrips(viewInfo);
}
public static Type GetNewTableType(ReportSpec reportSpec)
{
var rowTypes = new List<Type>();
foreach (var column in reportSpec.Select)
{
var rowType = GetRootTable(column);
if (null != rowType)
{
rowTypes.Add(rowType);
}
}
var unique = rowTypes.Distinct().ToArray();
if (unique.Length != 1)
{
return null;
}
return unique[0];
}
private bool TryGetReport(SrmDocument document, ReportSpec reportSpec, out string report)
{
lock (_cacheLock)
{
if (ReferenceEquals(document, _document) && _dictionary.TryGetValue(reportSpec, out report))
{
_list.Remove(reportSpec);
_list.AddFirst(reportSpec);
return true;
}
}
report = null;
return false;
}
public bool IsLast(ReportSpec report)
{
return _list.Last.Value.Equals(report);
}
/// <summary>
/// Returns the .csv file generated by exporting the given ReportSpec using data from the given Document.
/// </summary>
/// <param name="document">The current document open in Skyline</param>
/// <param name="reportSpec">The export report format</param>
/// <param name="progressMonitor"></param>
public string GetReport(SrmDocument document, ReportSpec reportSpec, IProgressMonitor progressMonitor)
{
string report;
if (TryGetReport(document, reportSpec, out report))
return report;
// Only on report at a time can be generated
lock (_reportGenLock)
{
// Try again, in case we were waiting for the report we want to be generated
if (TryGetReport(document, reportSpec, out report))
return report;
report = TestReport ?? reportSpec.ReportToCsvString(document, progressMonitor);
lock (_cacheLock)
{
// if the document has changed while the report was exporting, don't add it to the cache
if (ReferenceEquals(document, _document))
{
CurrentSize += ReportSize(report);
while (CurrentSize > (TestMaximumSize ?? MAXIMUM_SIZE))
{
// remove the oldest reports
ReportSpec oldestSpec = _list.Last.Value;
string oldestReport;
if (_dictionary.TryGetValue(oldestSpec, out oldestReport))
{
_dictionary.Remove(oldestSpec);
CurrentSize -= ReportSize(oldestReport);
}
_list.RemoveLast();
}
_list.AddFirst(reportSpec);
_dictionary.Add(reportSpec, report);
}
}
return report;
}
}
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 ViewInfo Convert(ReportSpec reportSpec)
{
var rootTable = GetRootTable(reportSpec);
if (null == rootTable)
{
return(null);
}
var columns = new List <ColumnSpec>();
var columnNames = new HashSet <PropertyPath>();
var sublistId = PropertyPath.Root;
foreach (var reportColumn in reportSpec.Select)
{
var columnSpec = ConvertReportColumn(reportColumn);
var collectionProperty = columnSpec.PropertyPath;
while (!collectionProperty.IsRoot && !collectionProperty.IsUnboundLookup)
{
collectionProperty = collectionProperty.Parent;
}
if (collectionProperty.StartsWith(sublistId))
{
sublistId = collectionProperty;
}
if (columnNames.Add(columnSpec.PropertyPath))
{
columns.Add(columnSpec);
}
}
if (null != reportSpec.GroupBy)
{
foreach (var reportColumn in reportSpec.GroupBy)
{
var columnSpec = ConvertReportColumn(reportColumn);
if (!columns.Any(col => Equals(col.PropertyPath, columnSpec.PropertyPath)))
{
columns.Add(columnSpec.SetHidden(true));
}
}
}
bool pivotIsotopeLabel = false;
if (null != reportSpec.CrossTabHeaders)
{
pivotIsotopeLabel =
reportSpec.CrossTabHeaders.Any(reportColumn => !reportColumn.Column.ToString().EndsWith(@"Replicate"));
if (pivotIsotopeLabel)
{
sublistId = PropertyPath.Root.Property(@"Results").LookupAllItems();
}
foreach (var reportColumn in reportSpec.CrossTabHeaders)
{
if (pivotIsotopeLabel || !reportColumn.Column.ToString().EndsWith(@"Replicate"))
{
var columnSpec = ConvertReportColumn(reportColumn).SetTotal(TotalOperation.PivotKey).SetHidden(true);
columns.Add(columnSpec);
}
}
}
if (null != reportSpec.CrossTabValues)
{
foreach (var reportColumn in reportSpec.CrossTabValues)
{
var convertedColumn = ConvertReportColumn(reportColumn);
if (pivotIsotopeLabel)
{
convertedColumn = convertedColumn.SetTotal(TotalOperation.PivotValue);
}
if (columnNames.Add(convertedColumn.PropertyPath))
{
columns.Add(convertedColumn);
}
}
}
var viewSpec = new ViewSpec()
.SetName(reportSpec.Name)
.SetSublistId(sublistId)
.SetColumns(columns)
.SetRowType(rootTable);
viewSpec = AddFilter(viewSpec, reportSpec);
return(new ViewInfo(DataSchema, rootTable, viewSpec));
}
public bool ContainsKey(ReportSpec reportSpec)
{
return(_dictionary.ContainsKey(reportSpec) && _list.Contains(reportSpec));
}
public bool IsLast(ReportSpec report)
{
return(_list.Last.Value.Equals(report));
}
public ViewInfo Convert(ReportSpec reportSpec)
{
var rootTable = GetRootTable(reportSpec);
if (null == rootTable)
{
return null;
}
var columns = new List<ColumnSpec>();
var columnNames = new HashSet<PropertyPath>();
var sublistId = PropertyPath.Root;
foreach (var reportColumn in reportSpec.Select)
{
var columnSpec = ConvertReportColumn(reportColumn);
var collectionProperty = columnSpec.PropertyPath;
while (!collectionProperty.IsRoot && !collectionProperty.IsUnboundLookup)
{
collectionProperty = collectionProperty.Parent;
}
if (collectionProperty.StartsWith(sublistId))
{
sublistId = collectionProperty;
}
if (columnNames.Add(columnSpec.PropertyPath))
{
columns.Add(columnSpec);
}
}
if (null != reportSpec.GroupBy)
{
foreach (var reportColumn in reportSpec.GroupBy)
{
var columnSpec = ConvertReportColumn(reportColumn);
if (!columns.Any(col => Equals(col.PropertyPath, columnSpec.PropertyPath)))
{
columns.Add(columnSpec.SetHidden(true));
}
}
}
bool pivotIsotopeLabel = false;
if (null != reportSpec.CrossTabHeaders)
{
pivotIsotopeLabel =
reportSpec.CrossTabHeaders.Any(reportColumn => !reportColumn.Column.ToString().EndsWith("Replicate")); // Not L10N
if (pivotIsotopeLabel)
{
sublistId = PropertyPath.Root.Property("Results").LookupAllItems(); // Not L10N
}
foreach (var reportColumn in reportSpec.CrossTabHeaders)
{
if (pivotIsotopeLabel || !reportColumn.Column.ToString().EndsWith("Replicate")) // Not L10N
{
var columnSpec = ConvertReportColumn(reportColumn).SetTotal(TotalOperation.PivotKey).SetHidden(true);
columns.Add(columnSpec);
}
}
}
if (null != reportSpec.CrossTabValues)
{
foreach (var reportColumn in reportSpec.CrossTabValues)
{
var convertedColumn = ConvertReportColumn(reportColumn);
if (pivotIsotopeLabel)
{
convertedColumn = convertedColumn.SetTotal(TotalOperation.PivotValue);
}
if (columnNames.Add(convertedColumn.PropertyPath))
{
columns.Add(convertedColumn);
}
}
}
var viewSpec = new ViewSpec()
.SetName(reportSpec.Name)
.SetSublistId(sublistId)
.SetColumns(columns)
.SetRowType(rootTable);
viewSpec = AddFilter(viewSpec, reportSpec);
return new ViewInfo(DataSchema, rootTable, viewSpec);
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(textName, out name))
return;
if (_columns.Count == 0)
{
MessageBox.Show(this, Resources.PivotReportDlg_OkDialog_A_report_must_have_at_least_one_column, Program.Name);
return;
}
ReportSpec reportSpec = GetReport().GetReportSpec(name);
if ((_reportSpec == null || !Equals(reportSpec.Name, _reportSpec.Name)) &&
_existing.Contains(reportSpec, new NameComparer<ReportSpec>()))
{
helper.ShowTextBoxError(textName, Resources.PivotReportDlg_OkDialog_The_report__0__already_exists, name);
return;
}
_reportSpec = reportSpec;
DialogResult = DialogResult.OK;
Close();
}
public void ReportToCsv(ReportSpec reportSpec, SrmDocument doc, string fileName)
{
CheckReportCompatibility.ReportToCsv(reportSpec, doc, fileName, LocalizationHelper.CurrentCulture);
}
public ReportOrViewSpec(ReportSpec reportSpec) : base(reportSpec.Name ?? NAME_INTERNAL)
{
ReportSpec = reportSpec;
}
public void ReportToCsv(ReportSpec reportSpec, SrmDocument doc, string fileName, CultureInfo cultureInfo)
{
CheckReportCompatibility.ReportToCsv(reportSpec, doc, fileName, cultureInfo);
}
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 ReportOrViewSpec(ReportSpec reportSpec) : base(reportSpec.Name)
{
ReportSpec = reportSpec;
}
