protected ReportInfo GetReportInfo(string path)
{
using (var stream = File.OpenRead(TestFilesDir.GetTestPath(path)))
{
return(new ReportInfo(path, ReportSharing.DeserializeReportList(stream)));
}
}
/// <summary>
/// Generate the list of Existing Reports that would be modified and the list of new reports
/// </summary>
private static List <ReportOrViewSpec> FindReportConflicts(DirectoryInfo toolInfDir, string tempToolPath, out List <ReportOrViewSpec> newReports)
{
var existingReports = new List <ReportOrViewSpec>();
newReports = new List <ReportOrViewSpec>();
foreach (FileInfo file in toolInfDir.GetFiles(@"*" + ReportSpecList.EXT_REPORTS))
{
List <ReportOrViewSpec> loadedItems;
try
{
using (var stream = File.OpenRead(file.FullName))
{
loadedItems = ReportSharing.DeserializeReportList(stream);
}
}
catch (Exception exception)
{
DirectoryEx.SafeDelete(tempToolPath);
throw new IOException(
string.Format(Resources.SerializableSettingsList_ImportFile_Failure_loading__0__,
file.FullName), exception);
}
var externalToolReports =
Settings.Default.PersistedViews.GetViewSpecList(PersistedViews.ExternalToolsGroup.Id);
Dictionary <string, ViewSpec> allExistingReports = new Dictionary <string, ViewSpec>();
if (externalToolReports != null)
{
foreach (var viewSpec in externalToolReports.ViewSpecs)
{
allExistingReports[viewSpec.Name] = viewSpec;
}
}
foreach (var reportOrViewSpec in loadedItems)
{
ViewSpec existingView;
if (allExistingReports.TryGetValue(reportOrViewSpec.GetKey(), out existingView))
{
if (!ReportSharing.AreEquivalent(reportOrViewSpec, new ReportOrViewSpec(existingView)))
{
existingReports.Add(reportOrViewSpec);
}
else
{
newReports.Add(reportOrViewSpec);
}
}
else
{
newReports.Add(reportOrViewSpec);
}
}
// We now have the list of Reports that would have a naming conflict.
}
return(existingReports);
}
private static List <ReportOrViewSpec> GetReportsFromFiles(DirectoryInfo toolInfDir, string tempToolPath)
{
var srmSerialzer = new XmlSerializer(typeof(SrmDocument));
var loadedItems = new List <ReportOrViewSpec>();
var skyrFiles = toolInfDir.GetFiles(@"*" + ReportSpecList.EXT_REPORTS);
if (skyrFiles.Length > 0)
{
foreach (FileInfo file in skyrFiles)
{
try
{
using (var stream = File.OpenRead(file.FullName))
{
loadedItems.AddRange(ReportSharing.DeserializeReportList(stream));
}
}
catch (Exception exception)
{
DirectoryEx.SafeDelete(tempToolPath);
throw new IOException(
string.Format(Resources.SerializableSettingsList_ImportFile_Failure_loading__0__,
file.FullName), exception);
}
}
}
else
{
foreach (FileInfo file in toolInfDir.GetFiles().Where(file => file.Extension.Equals(SrmDocument.EXT)))
{
SrmDocument document;
try
{
using (var stream = File.OpenRead(file.FullName))
{
document = (SrmDocument)srmSerialzer.Deserialize(stream);
}
}
catch (Exception exception)
{
throw new IOException(string.Format(
Resources.SerializableSettingsList_ImportFile_Failure_loading__0__,
file.FullName), exception);
}
var reports = document.Settings.DataSettings.ViewSpecList.ViewSpecLayouts;
foreach (ViewSpecLayout report in reports)
{
loadedItems.Add(new ReportOrViewSpec(report));
}
}
}
return(loadedItems);
}
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 TestGenerateMsStatsInput()
{
SrmDocument testDocument = OpenTestDocument();
var memoryDocumentContainer = new MemoryDocumentContainer();
Assert.IsTrue(memoryDocumentContainer.SetDocument(testDocument, memoryDocumentContainer.Document));
SkylineDataSchema skylineDataSchema = new SkylineDataSchema(memoryDocumentContainer, DataSchemaLocalizer.INVARIANT);
var view = ReportSharing.DeserializeReportList(OpenTestFile("MSstats_report.skyr")).First().ViewSpec;
var viewContext = new DocumentGridViewContext(skylineDataSchema);
StringWriter stringWriter = new StringWriter();
IProgressStatus progressStatus = new ProgressStatus();
viewContext.Export(new SilentProgressMonitor(), ref progressStatus,
viewContext.GetViewInfo(ViewGroup.BUILT_IN, view), stringWriter,
viewContext.GetCsvWriter());
string expectedReport = new StreamReader(OpenTestFile("BrudererSubset_MSstatsInput.csv")).ReadToEnd();
AssertEx.NoDiff(expectedReport, stringWriter.ToString());
}
/// <summary>
/// Generate the list of Existing Reports that would be modified and the list of new reports
/// </summary>
private static List <ReportOrViewSpec> FindReportConflicts(DirectoryInfo toolInfDir, string tempToolPath, out List <ReportOrViewSpec> newReports)
{
var existingReports = new List <ReportOrViewSpec>();
newReports = new List <ReportOrViewSpec>();
var externalToolReports =
Settings.Default.PersistedViews.GetViewSpecList(PersistedViews.ExternalToolsGroup.Id);
Dictionary <string, ViewSpecLayout> allExistingReports = new Dictionary <string, ViewSpecLayout>();
if (externalToolReports != null)
{
foreach (var viewSpec in externalToolReports.ViewSpecLayouts)
{
allExistingReports[viewSpec.Name] = viewSpec;
}
}
var loadedItems = GetReportsFromFiles(toolInfDir, tempToolPath);
foreach (var reportOrViewSpec in loadedItems)
{
ViewSpecLayout existingView;
if (allExistingReports.TryGetValue(reportOrViewSpec.GetKey(), out existingView))
{
if (!ReportSharing.AreEquivalent(reportOrViewSpec, new ReportOrViewSpec(existingView)))
{
existingReports.Add(reportOrViewSpec);
}
else
{
newReports.Add(reportOrViewSpec);
}
}
else
{
newReports.Add(reportOrViewSpec);
}
}
// We now have the list of Reports that would have a naming conflict.
return(existingReports);
}
public string GetReportFromDefinition(string reportDefinition)
{
var memoryStream = new MemoryStream(Encoding.UTF8.GetBytes(reportDefinition));
var reportOrViewSpecList = ReportSharing.DeserializeReportList(memoryStream);
if (reportOrViewSpecList.Count == 0)
{
throw new ArgumentException(@"No report definition found");
}
if (reportOrViewSpecList.Count > 1)
{
throw new ArgumentException(@"Too many report definitions");
}
var reportOrViewSpec = reportOrViewSpecList.First();
if (null == reportOrViewSpec.ViewSpec)
{
throw new ArgumentException(@"The report definition uses the old format.");
}
return(GetReportRows(Program.MainWindow.Document, reportOrViewSpec.ViewSpec, Program.MainWindow));
}
private static void AddToolFromProperties(FileInfo file,
UnzipToolReturnAccumulator accumulator,
ToolInfo toolInfo,
string placeHolderToolPath,
string tempToolPath,
IDictionary <string, string> reportRenameMapping)
{
if (file.Name == INFO_PROPERTIES)
{
return;
}
ExternalToolProperties readin;
try
{
readin = new ExternalToolProperties(file.FullName);
}
catch (Exception)
{
//Failed to read the .properties file
accumulator.AddMessage(string.Format(Resources.ConfigureToolsDlg_unpackZipTool_Failed_to_process_file_0_The_tool_described_failed_to_import,
file.Name));
return;
}
if (readin.Title == null || readin.Command == null)
{
accumulator.AddMessage(string.Format(TextUtil.LineSeparate(
Resources.ConfigureToolsDlg_unpackZipTool_Invalid_Tool_Description_in_file__0__,
Resources.ConfigureToolsDlg_unpackZipTool_Title_and_Command_are_required,
Resources.ConfigureToolsDlg_unpackZipTool_skipping_that_tool_), file.Name));
return;
}
string command = ProcessCommand(readin, tempToolPath, accumulator);
if (string.IsNullOrEmpty(command))
{
return;
}
string reportTitle = readin.Input_Report_Name;
List <AnnotationDef> annotations = new List <AnnotationDef>();
// Check we have the relevant report
if (!string.IsNullOrWhiteSpace(reportTitle))
{
if (reportRenameMapping.ContainsKey(reportTitle))
{
//Apply report renaming if install in parallel was selectedd
reportTitle = reportRenameMapping[reportTitle];
}
// Check if they are still missing the report they want
if (!ReportSharing.GetExistingReports().ContainsKey(PersistedViews.ExternalToolsGroup.Id.ViewName(reportTitle)))
{
accumulator.AddMessage(string.Format(Resources.UnpackZipToolHelper_UnpackZipTool_The_tool___0___requires_report_type_titled___1___and_it_is_not_provided__Import_canceled_,
readin.Title, reportTitle));
return;
}
// Get annotations for this specific tool
GetAnotations(readin, annotations);
}
//Check the ArgsCollector Dll exists.
string dllPath = readin.Args_Collector_Dll;
if (!string.IsNullOrEmpty(dllPath))
{
// Handle case where they prepended the DllPath with $(ToolDir)\\.
// ReSharper disable once LocalizableElement
if (dllPath.StartsWith(ToolMacros.TOOL_DIR + "\\"))
{
dllPath = dllPath.Substring(ToolMacros.TOOL_DIR.Length + 1);
}
if (!File.Exists(Path.Combine(tempToolPath, dllPath)))
{
accumulator.AddMessage(string.Format(Resources.ToolInstaller_AddToolFromProperties_Missing_the_file__0___Tool__1__import_failed, dllPath,
readin.Title));
return;
}
// Path to the dll gets renamed at the end of the UnpackZipTools Function when we
// finally decide the directory for the $(ToolDir)
}
//Make sure tools get a unique title.
string uniqueTitle = GetUniqueToolTitle(readin.Title);
//Append each tool to the return value
accumulator.AddTool(new ToolDescription(uniqueTitle,
command,
readin.Arguments,
readin.Initial_Directory,
readin.Output_to_Immediate_Window.Contains(@"True"),
reportTitle,
dllPath,
readin.Args_Collector_Type,
placeHolderToolPath,
annotations,
toolInfo.PackageVersion,
toolInfo.PackageIdentifier,
toolInfo.PackageName));
}
/// <summary>
/// Function for unpacking zipped External tools.
/// </summary>
/// <param name="pathToZip">Path to the zipped file that contains the tool and all its assicaited files.</param>
/// <param name="unpackSupport"> Interface that implements required functions that are dependent on context.</param>
/// <returns></returns>
public static UnzipToolReturnAccumulator UnpackZipTool(string pathToZip, IUnpackZipToolSupport unpackSupport)
{
if (!Directory.Exists(pathToZip) && !File.Exists(pathToZip))
{
throw new FileNotFoundException(pathToZip);
}
//Removes any old folders that dont have Tools associated with them
CheckToolDirConsistency();
var retval = new UnzipToolReturnAccumulator();
string name = Path.GetFileNameWithoutExtension(pathToZip);
if (name == null)
{
throw new ToolExecutionException(Resources.ConfigureToolsDlg_unpackZipTool_Invalid_file_selected__No_tools_added_);
}
// This helps with zipfiles that have spaces in the titles.
// Consider: We may want to add quotes around usages of the $(ToolDir) macro incase the Tool directory has spaces in one of its directory names.
name = name.Replace(' ', '_');
string outerToolsFolderPath = ToolDescriptionHelpers.GetToolsDirectory();
if (string.IsNullOrEmpty(outerToolsFolderPath))
{
throw new ToolExecutionException(Resources.ConfigureToolsDlg_unpackZipTool_Error_unpacking_zipped_tools);
}
string tempFolderPath = Path.Combine(outerToolsFolderPath, @"Temp");
var toolDir = new DirectoryInfo(tempFolderPath);
if (!toolDir.Exists)
{
toolDir.Create();
}
// This naming conflict shouldn't happen. The temp file should be empty.
// Consider: Try to delete the existing directory in the temp directory.
string tempToolPath = Path.Combine(tempFolderPath, name);
if (Directory.Exists(tempToolPath))
{
tempToolPath = DirectoryEx.GetUniqueName(tempToolPath);
}
using (new TemporaryDirectory(tempToolPath))
{
if (Directory.Exists(pathToZip))
{
DirectoryCopy(pathToZip, tempToolPath);
}
else
{
using (var zipFile = new ZipFile(pathToZip))
{
try
{
zipFile.ExtractAll(tempToolPath, ExtractExistingFileAction.OverwriteSilently);
}
catch (Exception)
{
throw new ToolExecutionException(Resources.ConfigureToolsDlg_unpackZipTool_There_is_a_naming_conflict_in_unpacking_the_zip__Tool_importing_canceled_);
}
}
}
var dirInfo = new DirectoryInfo(tempToolPath);
if (!dirInfo.Exists)
{
// Case where they try to load tools from an empty zipfile then the folder is never created.
dirInfo.Create();
}
var toolInfDir = new DirectoryInfo(Path.Combine(tempToolPath, TOOL_INF));
if (!toolInfDir.Exists)
{
throw new ToolExecutionException(TextUtil.LineSeparate(
Resources.ToolInstaller_UnpackZipTool_The_selected_zip_file_is_not_an_installable_tool_,
string.Format(Resources.ToolInstaller_UnpackZipTool_Error__It_does_not_contain_the_required__0__directory_, TOOL_INF)));
}
// Handle info.properties
var toolInfo = GetToolInfo(toolInfDir, retval);
if (!HandleAnnotations(unpackSupport.ShouldOverwriteAnnotations, toolInfDir))
{
return(null);
}
HandleLegacyQuaSAR(toolInfo);
var toolsToBeOverwritten = GetToolsToBeOverwritten(toolInfo.PackageIdentifier);
List <ReportOrViewSpec> newReports;
var existingReports = FindReportConflicts(toolInfDir, tempToolPath, out newReports);
bool?overwrite = IsOverwrite(unpackSupport.ShouldOverwrite, toolsToBeOverwritten, existingReports, toolInfo);
if (!overwrite.HasValue)
{
// User canceled installation.
return(null);
}
string DirectoryToRemove = null;
if (overwrite.Value)
{
// Delete the tools and their containing folder
if (toolsToBeOverwritten.Count > 0)
{
foreach (var tool in toolsToBeOverwritten)
{
Settings.Default.ToolList.Remove(tool);
}
// The tools are all guarenteed to be from the same directory by GetToolsToBeOverwritten
// and all toolDescriptions in a directory come from the same installation
DirectoryToRemove = toolsToBeOverwritten.First().ToolDirPath;
}
// Overwrite all existing reports.
foreach (ReportOrViewSpec item in existingReports)
{
ReportSharing.SaveReport(PersistedViews.ExternalToolsGroup, item);
}
}
// Add all new reports.
foreach (ReportOrViewSpec item in newReports)
{
ReportSharing.SaveReport(PersistedViews.ExternalToolsGroup, item);
}
var reportRenameMapping = new Dictionary <string, string>();
if (overwrite == false) // Dont overwrite so rename reports.
{
// Deal with renaming reports!
foreach (ReportOrViewSpec item in existingReports)
{
string oldname = item.GetKey();
string newname = GetUniqueReportName(oldname);
reportRenameMapping.Add(oldname, newname);
ReportSharing.SaveReportAs(PersistedViews.ExternalToolsGroup, item, newname);
}
}
foreach (FileInfo file in toolInfDir.GetFiles(@"*.properties"))
{
// We will replace the tool Directory value (null below) later when we know the import is sucessful.
AddToolFromProperties(file, retval, toolInfo, null, tempToolPath, reportRenameMapping);
}
// Check if we need to install a program
if (retval.Installations.Count > 0)
{
foreach (var ppc in retval.Installations.Keys)
{
string pathToPackageInstallScript = null;
if (ppc.ProgramName.Equals(@"R") && retval.Installations[ppc].Count != 0)
{
pathToPackageInstallScript = Path.Combine(tempToolPath, TOOL_INF, INSTALL_R_PACKAGES);
if (!File.Exists(pathToPackageInstallScript))
{
throw new ToolExecutionException(TextUtil.LineSeparate(string.Format(Resources.ToolInstaller_UnpackZipTool_Error__There_is_a_file_missing_the__0__zip, name),
string.Empty,
string.Format(Resources.ToolInstaller_UnpackZipTool_Tool_Uses_R_and_specifies_Packages_without_an__0__file_in_the_tool_inf_directory_, INSTALL_R_PACKAGES)));
}
}
string path = unpackSupport.InstallProgram(ppc, retval.Installations[ppc], pathToPackageInstallScript);
if (path == null)
{
// Cancel installation
return(null);
}
else if (path != string.Empty)
{
if (Settings.Default.ToolFilePaths.ContainsKey(ppc))
{
Settings.Default.ToolFilePaths.Remove(ppc);
}
Settings.Default.ToolFilePaths.Add(ppc, path);
}
}
}
// We don't decide the final toolDirPath until we make it to here.
// This will require some fixing of the tooldir and path to dll in each of the tools in retval.validtoolsfound
// It also enables us to not delete the tools from the tool list unless we have a sucessful installation.
// Decide the permToolPath.
if (DirectoryToRemove != null)
{
DirectoryEx.SafeDelete(DirectoryToRemove);
}
// Final Directory Location.
string permToolPath = DirectoryEx.GetUniqueName(Path.Combine(outerToolsFolderPath, name));
foreach (var tool in retval.ValidToolsFound)
{
tool.ToolDirPath = permToolPath;
if (!string.IsNullOrEmpty(tool.ArgsCollectorDllPath))
{
tool.ArgsCollectorDllPath = Path.Combine(permToolPath, tool.ArgsCollectorDllPath);
}
Settings.Default.ToolList.Add(tool);
}
if (retval.ValidToolsFound.Count != 0)
{
Helpers.TryTwice(() => Directory.Move(tempToolPath, permToolPath));
}
}
return(retval);
}
/// <summary>
/// Construct a new PersistedViews, migrating over the values from the old ViewSpecList
/// and ReportSpecList properties. Views that are in use by an external tool get put in
/// the External Tools group, and views that are
/// </summary>
public PersistedViews(ReportSpecList reportSpecList, ViewSpecList viewSpecList, ToolList toolList)
{
var viewItems = new List <ViewSpec>();
if (null != viewSpecList)
{
viewItems.AddRange(viewSpecList.ViewSpecs);
}
if (null != reportSpecList)
{
RevisionIndex = reportSpecList.RevisionIndex + 1;
foreach (var newView in ReportSharing.ConvertAll(reportSpecList.Select(reportSpec => new ReportOrViewSpec(reportSpec)),
new SrmDocument(SrmSettingsList.GetDefault())))
{
if (viewItems.Any(viewSpec => viewSpec.Name == newView.Name))
{
continue;
}
viewItems.Add(newView);
}
}
var viewSpecLists = new Dictionary <ViewGroup, Dictionary <string, ViewSpec> >();
foreach (var viewItem in viewItems)
{
ViewGroup group;
if (toolList.Any(tool => tool.ReportTitle == viewItem.Name))
{
group = ExternalToolsGroup;
}
else
{
group = MainGroup;
}
Dictionary <string, ViewSpec> list;
if (!viewSpecLists.TryGetValue(group, out list))
{
list = new Dictionary <string, ViewSpec>();
viewSpecLists.Add(group, list);
}
if (!list.ContainsKey(viewItem.Name))
{
list.Add(viewItem.Name, viewItem);
}
else
{
for (int i = 1;; i++)
{
string name = viewItem.Name + i;
if (!list.ContainsKey(name))
{
list.Add(name, viewItem.SetName(name));
break;
}
}
}
}
foreach (var entry in viewSpecLists)
{
SetViewSpecList(entry.Key.Id, new ViewSpecList(entry.Value.Values));
}
AddDefaults();
}