private bool ValidateOutputDirectory(string outputFilePath)
{
try
{
var outputFile = new FileInfo(outputFilePath);
if (outputFile.Directory == null ||
outputFile.DirectoryName == null)
{
OnErrorEvent("Unable to determine the parent directory of output file: " + outputFile);
return(false);
}
if (!outputFile.Directory.Exists)
{
OnStatusEvent("Creating output directory: " + outputFile.Directory.FullName);
outputFile.Directory.Create();
}
return(true);
}
catch (Exception ex)
{
OnErrorEvent("Unable to determine the parent directory of output file: " + outputFilePath);
Console.WriteLine(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
return(false);
}
}
/// <summary>
/// this function controls the class behavior
/// </summary>
/// <param name="fileName">The command line file to run</param>
/// <param name="args">the parameters to pass to the program</param>
private void Init(string fileName, string args)
{
// create a process
var process = new Process();
// apply all required elements for process
var startInfo = new ProcessStartInfo(fileName, args)
{
RedirectStandardOutput = true,
RedirectStandardError = true,
UseShellExecute = false
};
process.StartInfo = startInfo;
try
{
// start the process
process.Start();
process.WaitForExit();
StandardOut = process.StandardOutput.ReadToEnd();
StandardError = process.StandardError.ReadToEnd();
// if error set status code
if (!process.ExitCode.Equals(0))
{
Status = StatusCode.Error;
}
}
catch (Exception ex)
{
Console.WriteLine("Error starting the process: " + ex.Message);
Console.WriteLine(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
// exception from process starting
Status = StatusCode.FileNotFound;
}
}
private static void ShowGUI()
{
Application.EnableVisualStyles();
Application.DoEvents();
try
{
var handle = GetConsoleWindow();
if (!mDebugMode)
{
// Hide the console
ShowWindow(handle, SW_HIDE);
}
var objFormMain = new GUI()
{
KeepDB = mKeepDB
};
objFormMain.ShowDialog();
if (!mDebugMode)
{
// Show the console
ShowWindow(handle, SW_SHOW);
}
}
catch (Exception ex)
{
ConsoleMsgUtils.ShowWarning("Error in ShowGUI: " + ex.Message);
ConsoleMsgUtils.ShowWarning(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
MessageBox.Show("Error in ShowGUI: " + ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
}
public string FormatStackTrace(string stackTraceText)
{
if (string.IsNullOrWhiteSpace(stackTraceText))
{
return(string.Empty);
}
string html;
try
{
var formattedStackTrace = StackTraceFormatter.FormatHtml(stackTraceText,
new StackTraceHtmlFragments
{
BeforeFrame = "<span class='frame'>",
AfterFrame = "</span>",
});
html = $"<pre><code>{formattedStackTrace}</code></pre>";
}
catch (Exception ex)
{
_logger.LogError(ex, $"Could not parse Stack Trace for \n{stackTraceText}");
html = $"Stack Trace could not be parsed/formatted:<br /> {ex.Message}";
}
return(html);
}
/// <summary>
/// The main entry point for the application.
/// </summary>
private static void Main()
{
// Start the main program running
try
{
if (mMainProcess == null)
{
mMainProcess = new MainProgram();
if (!mMainProcess.InitMgr())
{
PRISM.Logging.FileLogger.FlushPendingMessages();
return;
}
mMainProcess.DoDirectoryCreation();
}
}
catch (Exception ex)
{
var errMsg = "Critical exception starting application: " + ex.Message;
ConsoleMsgUtils.ShowWarning(errMsg + "; " + StackTraceFormatter.GetExceptionStackTrace(ex));
ConsoleMsgUtils.ShowWarning("Exiting clsMainProcess.Main with error code = 1");
}
PRISM.Logging.FileLogger.FlushPendingMessages();
}
public NonEscapedString StackTrace(string stackTrace)
{
try
{
return(new NonEscapedString(StackTraceFormatter.FormatHtml(stackTrace, StackTraceHtmlFragments)));
}
catch (RegexMatchTimeoutException)
{
return(new NonEscapedString(HtmlEncode(stackTrace)));
}
}
private void ShowStackTraceNow(IReadOnlyCollection <string> parents, int depth, bool multiLine)
{
Assert.AreEqual(depth, parents.Count, "Parent list length invalid");
string stackTrace;
if (multiLine)
{
stackTrace = StackTraceFormatter.GetCurrentStackTraceMultiLine();
}
else
{
stackTrace = StackTraceFormatter.GetCurrentStackTrace();
}
Console.WriteLine(stackTrace);
}
private void ShowErrorMessage(string message, Exception ex = null)
{
if (ex == null || message.Contains(ex.Message))
{
AppendProcessingStatus(message, true);
}
else
{
AppendProcessingStatus(message + ": " + ex.Message, true);
}
if (ex == null)
{
return;
}
var stackTrace = StackTraceFormatter.GetExceptionStackTraceMultiLine(ex, true, false);
AppendProcessingStatus(stackTrace, true);
}
public void VerifyExceptionStackTrace(ExceptionTypes targetException, int depth, bool multiLine, bool includeMethodParams = false)
{
var parents = new List <string>();
try
{
RecursiveMethodA(targetException, parents, 1, depth);
}
catch (Exception ex)
{
string stackTrace;
if (multiLine)
{
stackTrace = StackTraceFormatter.GetExceptionStackTraceMultiLine(ex, true, includeMethodParams);
}
else
{
stackTrace = StackTraceFormatter.GetExceptionStackTrace(ex);
}
Console.WriteLine(stackTrace);
}
}
/// <summary>
/// Initialization function that controls the program
/// </summary>
/// <param name="options">Processing options</param>
/// <returns>True on success, false if an error</returns>
private bool ProcessMetabolites(MetaboliteValidatorOptions options)
{
try
{
if (string.IsNullOrWhiteSpace(options.InputFile))
{
Console.WriteLine();
Console.WriteLine("Error, input file not defined");
return(false);
}
var inputFile = new FileInfo(options.InputFile);
if (!inputFile.Exists)
{
Console.WriteLine();
Console.WriteLine("Error, input file not found: " + inputFile.FullName);
return(false);
}
// init github api interaction with the repo and owner
var github = new Github("MetabolomicsCCS", "PNNL-Comp-Mass-Spec", options.Preview);
if (!string.IsNullOrEmpty(options.Username))
{
github.Username = options.Username;
if (!string.IsNullOrEmpty(options.Password))
{
if (options.Password.StartsWith("*"))
{
github.Password = MetaboliteValidatorOptions.DecodePassword(options.Password.Substring(1));
}
else
{
github.Password = options.Password;
}
}
}
// get main data file from github
var dataFile = github.GetFile("data/" + MASTER_TSV_FILE);
// parse the new data to append to current data
var fileToAppend = new DelimitedFileParser();
fileToAppend.ParseFile(inputFile.FullName, '\t');
Console.WriteLine();
Console.WriteLine("Found {0} records in local file {1}", fileToAppend.Count(), inputFile.Name);
// Update column names if necessary
UpdateHeaders(fileToAppend);
// parse the main data file from github
var mainFile = new DelimitedFileParser();
if (dataFile == null)
{
mainFile.SetDelimiter('\t');
mainFile.SetHeaders(fileToAppend.GetHeaders());
}
else
{
mainFile.ParseString(dataFile, '\t');
Console.WriteLine();
Console.WriteLine("Found {0} records in file {1} retrieved from GitHub", mainFile.Count(), MASTER_TSV_FILE);
Console.WriteLine();
}
// Update column names if necessary
UpdateHeaders(mainFile);
var duplicateRowCount = 0;
if (!options.IgnoreErrors)
{
// Get ids for Kegg and PubChem
var keggIds = fileToAppend.GetColumnAt("kegg").Where(x => !string.IsNullOrEmpty(x)).ToList();
var cidIds = fileToAppend.GetColumnAt("pubchem cid").Where(x => !string.IsNullOrEmpty(x)).ToList();
var mainCasIds = mainFile.GetColumnAt("cas").Where(x => !string.IsNullOrEmpty(x)).ToList();
// generate PubChem and Kegg utils
var pub = new PubchemUtil(cidIds.ToArray());
var kegg = new KeggUtil(keggIds.ToArray());
var file = new StreamWriter("ValidationApi.txt");
var dupRows = new DelimitedFileParser();
dupRows.SetHeaders(fileToAppend.GetHeaders());
dupRows.SetDelimiter('\t');
var warningRows = new DelimitedFileParser();
warningRows.SetHeaders(fileToAppend.GetHeaders());
warningRows.SetDelimiter('\t');
var missingKegg = new DelimitedFileParser();
missingKegg.SetHeaders(fileToAppend.GetHeaders());
missingKegg.SetDelimiter('\t');
var dataMap = fileToAppend.GetMap();
// compare fileToAppend to utils
for (var i = dataMap.Count - 1; i >= 0; i--)
{
Compound p = null;
CompoundData k = null;
if (!string.IsNullOrEmpty(dataMap[i]["pubchem cid"]))
{
p = pub.PubChemMap[int.Parse(dataMap[i]["pubchem cid"])];
}
if (!string.IsNullOrEmpty(dataMap[i]["kegg"]) && kegg.CompoundsMap.ContainsKey(dataMap[i]["kegg"]))
{
k = kegg.CompoundsMap[dataMap[i]["kegg"]];
}
if (mainCasIds.Contains(dataMap[i]["cas"]))
{
dupRows.Add(dataMap[i]);
fileToAppend.Remove(dataMap[i]);
}
else
{
if (k == null && CheckRow(dataMap[i], p, null))
{
missingKegg.Add(dataMap[i]);
}
else if (!CheckRow(dataMap[i], p, k))
{
// remove from list add to warning file
WriteContentToFile(file, dataMap[i], p, k, warningRows.Count() + 2);
warningRows.Add(dataMap[i]);
fileToAppend.Remove(dataMap[i]);
}
}
}
duplicateRowCount = dupRows.Count();
file.Close();
if (fileToAppend.Count() > 0)
{
Console.WriteLine("Validating data file with GoodTables");
var goodTables = new GoodTables(fileToAppend.ToString(true), SchemaUrl);
if (!goodTables.Response.success)
{
//foreach(var result in goodTables.Response.report.results)
//{
// fileToAppend.Remove(result["0"].result_context[0]);
//}
goodTables.OutputResponse(new StreamWriter(GOOD_TABLES_WARNING_FILE));
Console.WriteLine();
Console.WriteLine("GoodTables reports errors; see " + GOOD_TABLES_WARNING_FILE);
Console.WriteLine("Note that data with N/A in columns that expect a number will be flagged as an error by GoodTables; those errors can be ignored");
}
}
streamToFile(DUPLICATE_ROWS_FILE, dupRows);
streamToFile(WARNING_ROWS_FILE, warningRows);
streamToFile(MISSING_KEGG_FILE, missingKegg);
if (warningRows.Count() > 0)
{
Console.WriteLine();
Console.WriteLine("Warnings were encountered; see file " + WARNING_ROWS_FILE);
}
if (missingKegg.Count() > 0)
{
Console.WriteLine();
Console.WriteLine("Warnings were encountered; see file " + MISSING_KEGG_FILE);
}
}
else
{
Console.WriteLine();
Console.WriteLine("Ignoring validation, skipping to file upload.");
}
if (fileToAppend.Count() == 0)
{
Console.WriteLine();
Console.WriteLine("No new compounds were found; see {0} for the {1} skipped compounds", DUPLICATE_ROWS_FILE, duplicateRowCount);
}
else
{
// this will add the new data tsv to the existing tsv downloaded from github
var success = mainFile.Concat(fileToAppend);
if (!success)
{
// Concatenation of new records failed; do not upload
return(false);
}
// Start command line process for GoodTables
//
// string userDirPath = Environment.GetEnvironmentVariable("GOODTABLES_PATH");
// string commandLine = $"schema \"{options.InputFile}\" --schema \"{SchemaUrl}\"";
// string GoodTablesPath = $"{userDirPath}\\GoodTables";
//CommandLineProcess pro = new CommandLineProcess(GoodTablesPath, commandLine);
//// if error display errors and exit
//if (pro.Status.Equals(CommandLineProcess.StatusCode.Error))
//{
// Console.WriteLine($"GoodTables Validation error\n\n{pro.StandardOut}{pro.StandardError}\nExiting program please check that the data is valid.");
// Console.ReadKey();
// Environment.Exit(1);
//}
//// if the GoodTables.exe file isn't found display message and exit
//else if (pro.Status.Equals(CommandLineProcess.StatusCode.FileNotFound))
//{
// Console.WriteLine("File not found. Please make sure you have installed python and GoodTables.\n"
// +"Check that the folder path for GoodTables.exe is added to an environment variable named GOODTABLES_PATH.\n"
// +"Press any key to continue.");
// Console.ReadKey();
// Environment.Exit(1);
//}
//else
//{
// Console.WriteLine($"GoodTables validation\n\n{pro.StandardOut}");
//
// This will send the completed tsv back to github
github.SendFileAsync(mainFile.ToString(true), "data/" + MASTER_TSV_FILE);
// send Agilent file to github
github.SendFileAsync(mainFile.PrintAgilent(), "data/metabolitedataAgilent.tsv");
//}
}
return(true);
}
catch (Exception ex)
{
Console.WriteLine();
Console.WriteLine("Error processing data: " + ex.Message);
Console.WriteLine(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
return(false);
}
}
/// <summary>
/// 解析格式化字符串
/// </summary>
/// <param name="format"></param>
/// <returns></returns>
public static List <IPartFormatter> ParseFormat(string format)
{
int start = -1;
int tag = 0;
var parts = new List <string>();
int len = format.Length;
int idx = format.IndexOf('{');
parts.Add(format.Substring(0, idx));
for (int i = idx; i < len; ++i)
{
switch (format[i])
{
case '{':
if (start != -1)
{
parts.Add(format.Substring(start, i - start));
}
start = i;
break;
case '}':
parts.Add(format.Substring(start, i - start));
start = i + 1;
tag = start; //标记最后面的填充字符的开始位置
break;
}
}
parts.Add(format.Substring(tag, len - tag));
// {Date:yyyy-MM-dd HH:mm:ss.ffff} {ThreadId} {StackTrace:3,40} {Message}
var formatters = new List <IPartFormatter>();
foreach (string part in parts)
{
if (part.StartsWith("{DateTime"))
{
if (part.Length > 9 && part[9] == ':')
{
formatters.Add(new DateTimeFormatter {
FormatString = part.Substring(10)
});
}
else
{
formatters.Add(new DateTimeFormatter());
}
}
else if (part.StartsWith("{ThreadId"))
{
formatters.Add(new ThreadIdFormatter());
}
else if (part.StartsWith("{StackTrace"))
{
if (!part.StartsWith("{StackTrace:"))
{
formatters.Add(new StackTraceFormatter());
continue;
}
string[] subparts = part.Substring(12).Split(',');
var formatter = new StackTraceFormatter();
if (subparts.Length > 0)
{
formatter.Count = int.Parse(subparts[0]);
}
if (subparts.Length > 1)
{
formatter.PadLength = int.Parse(subparts[1]);
}
if (subparts.Length > 2)
{
formatter.SkipCount = int.Parse(subparts[2]);
}
formatters.Add(formatter);
}
else if (part.StartsWith("{Message"))
{
formatters.Add(new MessageFormatter());
}
else if (part.StartsWith("{LogLevel"))
{
formatters.Add(new LogLevelFormatter());
}
else
{
formatters.Add(new TextFormatter {
Text = part
});
}
}
return(formatters);
}
private static void ShowError(string message, Exception ex = null)
{
Console.WriteLine();
var msg = "Error: " + message;
ConsoleMsgUtils.ShowError(msg, ex);
mLogFile?.WriteLine(DateTime.Now.ToString("yyyy-MM-dd hh:mm:ss tt") + "\t" + msg);
if (ex != null)
{
mLogFile?.WriteLine(DateTime.Now.ToString("yyyy-MM-dd hh:mm:ss tt") + "\t" + StackTraceFormatter.GetExceptionStackTrace(ex));
}
}
private void LinuxSystemInfo_ErrorEvent(string message, Exception ex)
{
Console.WriteLine("Error: " + message);
Console.WriteLine(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
}
public override void Execute()
{
WriteLiteral("\r\n");
#line 5 "..\..\Views\Dashboard\LogInfo.cshtml"
var log = (ILogModel)ViewData["Model"];
#line default
#line hidden
WriteLiteral(@"<div class=""container-fluid"">
<div class=""mb-4 open"">
<ul class=""nav nav-tabs"" role=""tablist"">
<li class=""nav-item"">
<a class=""nav-link active"" data-toggle=""tab"" href=""#overview"" role=""tab"" aria-controls=""overview"" aria-selected=""true"">概览</a>
</li>
<li class=""nav-item"">
<a class=""nav-link"" data-toggle=""tab"" href=""#environment"" role=""tab"" aria-controls=""environment"" aria-selected=""false"">其他</a>
</li>
");
#line 19 "..\..\Views\Dashboard\LogInfo.cshtml"
if (typeof(IRequestTraceLogModel).IsAssignableFrom(Context.Options.LogModelType))
{
#line default
#line hidden
WriteLiteral(" <li class=\"nav-item\">\r\n\r\n <a class=\"na" +
"v-link\" data-toggle=\"tab\" href=\"#requestTrace\" role=\"tab\" aria-controls=\"request" +
"Trace\" onclick=\"requestTrace(\'");
#line 24 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.Id.ToString());
#line default
#line hidden
WriteLiteral("\')\" aria-selected=\"false\">请求追踪</a>\r\n </li>\r\n");
#line 26 "..\..\Views\Dashboard\LogInfo.cshtml"
}
#line default
#line hidden
WriteLiteral(@" </ul>
<div class=""tab-content"">
<div class=""tab-pane active"" id=""overview"" role=""tabpanel"">
<div class=""table-responsive"">
<table class=""table table-bordered"">
<tbody>
<tr>
<td>Id</td>
<td class=""text-nowrap"">");
#line 37 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.Id.ToString());
#line default
#line hidden
WriteLiteral("</td>\r\n </tr>\r\n <tr>\r\n " +
" <td>时间</td>\r\n <td clas" +
"s=\"text-nowrap\">");
#line 41 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.LongDate.ToString("yyyy-MM-dd HH:mm:ss"));
#line default
#line hidden
WriteLiteral("</td>\r\n </tr>\r\n <tr>\r\n " +
" <td>级别</td>\r\n <td clas" +
"s=\"text-nowrap\"><button class=\"btn btn-outline-");
#line 45 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.Level.ToUpper());
#line default
#line hidden
WriteLiteral("\">");
#line 45 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.Level.ToUpper());
#line default
#line hidden
WriteLiteral("</button></td>\r\n </tr>\r\n <t" +
"r>\r\n <td>Logger</td>\r\n " +
" <td class=\"text-nowrap\">");
#line 49 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.Logger);
#line default
#line hidden
WriteLiteral("</td>\r\n </tr>\r\n <tr>\r\n " +
" <td>消息</td>\r\n <td clas" +
"s=\"text-nowrap\">");
#line 53 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(log.Message);
#line default
#line hidden
WriteLiteral(@"</td>
</tr>
</tbody>
</table>
<div class=""card"">
<div class=""card-header bg-light"">
堆栈信息
</div>
<div class=""card-body"">
<pre>");
#line 63 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(Raw(StackTraceFormatter.FormatHtml(log.Exception)));
#line default
#line hidden
WriteLiteral(@"</pre>
</div>
</div>
</div>
</div>
<div class=""tab-pane"" id=""environment"" role=""tabpanel"">
<div class=""table-responsive"">
<table class=""table table-bordered"">
<tbody>
");
#line 73 "..\..\Views\Dashboard\LogInfo.cshtml"
foreach (var propertyInfo in Context.Options.CustomPropertyInfos)
{
#line default
#line hidden
WriteLiteral(" <tr>\r\n " +
" <td style=\"width: 13%\">");
#line 77 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(propertyInfo.Name);
#line default
#line hidden
WriteLiteral("</td>\r\n <td class=\"text-nowrap\">");
#line 78 "..\..\Views\Dashboard\LogInfo.cshtml"
Write(propertyInfo.GetValue(log));
#line default
#line hidden
WriteLiteral("</td>\r\n </tr>\r\n");
#line 80 "..\..\Views\Dashboard\LogInfo.cshtml"
}
#line default
#line hidden
WriteLiteral(@" </tbody>
</table>
</div>
</div>
<div class=""tab-pane"" id=""requestTrace"" role=""tabpanel"">
<div class=""table-responsive"">
<div id=""traceLogList"">
</div>
</div>
</div>
</div>
</div>
</div>");
}
public NonEscapedString StackTrace(string stackTrace)
{
return(new NonEscapedString(StackTraceFormatter.FormatHtml(stackTrace, StackTraceHtmlFragments)));
}
