/// <summary>
/// process result files collected and generate the CCS/mz DB.
/// </summary>
/// <param name="analysisDirectory">
/// The analysis directory.
/// </param>
/// <exception cref="Exception">
/// </exception>
public void ProcessResultFiles(string analysisDirectory, AnalysisLibrary lib)
{
long count = 0;
long totalTasks = this.Tasks.Count();
foreach (ImsInformedProcess task in this.Tasks)
{
// Deserialize the results and dispatch them into lookup tables.
try
{
IList<CrossSectionWorkflowResult> results = task.DeserializeResultBinFile();
AsyncHelpers.RunSync(() => lib.InsertResult(results));
count++;
Console.WriteLine("Number of results processed: {0}/{1}", count, totalTasks);
Console.SetCursorPosition(0, Console.CursorTop - 1);
// Dispose the task as it is no longer used.
task.Dispose();
}
catch (Exception e)
{
Console.WriteLine("Result processing for {0} failed", task.DataSetName);
Console.WriteLine("Exception: {0}", e.Message);
Console.WriteLine(string.Empty);
}
}
this.empty = false;
}
public async static void AnalysisDBTest()
{
var snapshot1 = new ArrivalTimeSnapShot();
snapshot1.DriftTubeVoltageInVolt = 1000;
snapshot1.MeasuredArrivalTimeInMs = 22;
snapshot1.PressureInTorr = 4;
snapshot1.TemperatureInKelvin = 10;
var iso1 = new IdentifiedIsomerInfo(2 ,222, 0.9, 10.5, 115, 123, new List<ArrivalTimeSnapShot>(){snapshot1}, 100, AnalysisStatus.Positive, new PeakScores(1.0, 0.8, 0.7), new MolecularTarget("C2H4O16P2", IonizationMethod.Protonated, "testamin"), 0.1, 0);
var idens = new List<IdentifiedIsomerInfo>() {iso1};
PeakScores scores = new PeakScores(0, 0.5, 1);
CrossSectionWorkflowResult result1 = new CrossSectionWorkflowResult("ABC_Dataset_01", new MolecularTarget("C2H4O16P2", IonizationMethod.Protonated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.2), scores, 0.5, OutputFileDir, "123");
CrossSectionWorkflowResult result2 = new CrossSectionWorkflowResult("ABC_Dataset_02", new MolecularTarget("C2H4O16P2", IonizationMethod.Protonated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result3 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C2H4O16P2", IonizationMethod.Deprotonated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), idens, scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result4 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C2H4O16P2", IonizationMethod.Sodiumated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), idens, scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result5 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C10H40", IonizationMethod.Protonated, "googlin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), idens, scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result6 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C10H40", IonizationMethod.Protonated, "googlin"), AnalysisStatus.Negative, null, idens, scores, 0.8, OutputFileDir, "123");
string fileName = @"output\test.sqlite";
AnalysisLibrary lib = new AnalysisLibrary(fileName);
await lib.CreateTables();
await lib.InsertResult(result1);
await lib.InsertResult(result2);
await lib.InsertResult(result3);
await lib.InsertResult(result4);
await lib.InsertResult(result5);
await lib.InsertResult(result6);
}
public static void Main(string[] args)
{
try
{
// Check if PIXIE.exe is present.
string exe = "PIXIE.exe";
if (!File.Exists(exe))
{
throw new FileNotFoundException("PIXIE.exe not found in directory " + Directory.GetCurrentDirectory() + "Please double check installation");
}
var options = new Options();
if (Parser.Default.ParseArguments(args, options))
{
string searchSpecPath = options.SearchSpecFile;
// Check if searchSpec file exisits.
if (!File.Exists(searchSpecPath))
{
throw new FileNotFoundException("Search spec file: " + searchSpecPath + " not found");
}
if (!Directory.Exists(options.InputPath))
{
throw new FileNotFoundException("Input path does not exist", options.InputPath);
}
if (!string.IsNullOrEmpty(options.OutputPath))
{
if (!Directory.Exists(options.OutputPath))
{
Directory.CreateDirectory(options.OutputPath);
}
}
int maxNumberOfProcesses = options.NumberOfProcesses;
bool reanalyze = options.Reanalyze;
string workspaceDir = string.IsNullOrEmpty(options.OutputPath) ? options.InputPath : options.OutputPath;
// Process the search spec file
try
{
TextSearchSpecProcessor processor = new TextSearchSpecProcessor(exe, searchSpecPath, options.InputPath, options.OutputPath, options.ShowWindow, options.IgnoreMissingFiles);
// Run the program in a single process.
int numberOfCommands = processor.TaskList.Count;
int count = 0;
int index = 0;
HashSet<ImsInformedProcess> runningTasks = new HashSet<ImsInformedProcess>();
List<ImsInformedProcess> failedAnalyses = new List<ImsInformedProcess>();
AnalysisLibrary lib = new AnalysisLibrary(Path.Combine(options.OutputPath, "analysesDB.sqlite"));
AsyncHelpers.RunSync(() => lib.CreateTables());
while (count < numberOfCommands)
{
if (runningTasks.Count < maxNumberOfProcesses)
{
// Find the next non-conflicting task that is not done yet and resource-free and is not running.
bool done = processor.TaskList[index].Done;
bool running = runningTasks.Contains(processor.TaskList[index]);
bool resourceFree = processor.TaskList[index].AreResourcesFree(runningTasks);
while (done || running || !resourceFree)
{
if (index + 1 == numberOfCommands)
{
ImsInformedProcess doneProcess = WaitUntilAtLeastOneTaskDone(runningTasks);
ProcessFinishedTask(doneProcess, failedAnalyses);
index = 0;
}
else
{
index++;
}
done = processor.TaskList[index].Done;
running = runningTasks.Contains(processor.TaskList[index]);
resourceFree = processor.TaskList[index].AreResourcesFree(runningTasks);
}
runningTasks.Add(processor.TaskList[index]);
if (!File.Exists(processor.TaskList[index].ResultBinFile) || reanalyze)
{
string outputDir = Path.GetDirectoryName(processor.TaskList[index].ResultBinFile);
if (outputDir != null && Directory.Exists(outputDir))
{
DirectoryInfo di = new DirectoryInfo(outputDir);
FileInfo[] files = di.GetFiles("*.png")
.Where(p => p.Extension == ".png").ToArray();
foreach (FileInfo file in files)
{
file.Attributes = FileAttributes.Normal;
File.Delete(file.FullName);
}
}
processor.TaskList[index].Start();
Console.WriteLine("Initiating Analysis Job [ID = {0}] out of {1} jobs.", processor.TaskList[index].JobID, numberOfCommands);
Console.WriteLine("Dataset Name: " + processor.TaskList[index].DataSetName);
Console.WriteLine("Running " + processor.TaskList[index].StartInfo.FileName + " " + processor.TaskList[index].StartInfo.Arguments);
Console.WriteLine(" ");
}
else
{
// skip the given analysis job
processor.TaskList[index].Done = true;
ProcessFinishedTask(processor.TaskList[index], failedAnalyses);
}
count++;
}
else if (runningTasks.Count == maxNumberOfProcesses)
{
ImsInformedProcess doneProcess = WaitUntilAtLeastOneTaskDone(runningTasks);
ProcessFinishedTask(doneProcess, failedAnalyses);
}
}
// Wait until runningTasks is empty
foreach (var item in runningTasks)
{
if (!item.Done)
{
item.WaitForExit();
item.Done = true;
if (item.ExitCode == 0)
{
Console.WriteLine("Analysis completed succeessfully for (ID =" + item.JobID + ") " + item.DataSetName);
}
else
{
Console.WriteLine("Analysis failed for (ID =" + item.JobID + ") " + item.DataSetName + ". Check the error file for details.");
failedAnalyses.Add(item);
}
}
else
{
ProcessFinishedTask(item, failedAnalyses);
Console.WriteLine("Analysis was completed before and Reanalyze setting is on, skipping analysis for (ID =" + item.JobID + ") " + item.DataSetName);
}
Console.WriteLine(" ");
}
// Collect result from result files
Console.WriteLine("Aggregating Analyses Results...");
IEnumerable<ImsInformedProcess> sortedTasks = processor.TaskList;
ResultAggregator resultAggregator = new ResultAggregator(sortedTasks);
resultAggregator.ProcessResultFiles(workspaceDir, lib);
Console.WriteLine("Aggregating Analyses Done");
Console.WriteLine();
// Print analysis result to console and summary file.
string summaryFilePath = Path.Combine(workspaceDir, "analysis_summary.txt");
// Setup result file.
Trace.Listeners.Clear();
ConsoleTraceListener consoleTraceListener = new ConsoleTraceListener(false);
consoleTraceListener.TraceOutputOptions = TraceOptions.DateTime;
}
catch (AggregateException e)
{
foreach (Exception exception in e.InnerExceptions)
{
if (exception.Data.Contains("lineNumber"))
{
Console.Write("Line {0}: ", exception.Data["lineNumber"]);
}
Console.WriteLine(exception.Message);
Console.WriteLine(string.Empty);
}
Console.WriteLine(e.Message);
Console.WriteLine();
}
}
}
catch (Exception e)
{
Console.WriteLine(e.Message);
Console.WriteLine(e.StackTrace);
Console.WriteLine(String.Empty);
}
Console.WriteLine("Press any key to exit...");
Console.ReadKey();
}
