示例#1
0
 private void DoSaveResultsToFile(UIsettings fixedSettings, ResultItems results)
 {
     if (fixedSettings.UseStorageFile)
     {
         string filePath = Path.GetDirectoryName(fixedSettings.Storagefile);
         if (!Directory.Exists(filePath))
         {
             Log.Error("[" + fixedSettings.Storagefile + "] Something is wrong with the file destination, skipping saving of results");
         }
         else if (!File.Exists(fixedSettings.Storagefile))
         {
             Log.Information("[" + fixedSettings.Storagefile + "] Creating file and writing results");
             using (StreamWriter fileStream = new StreamWriter(fixedSettings.Storagefile))
             {
                 fileStream.WriteLine(String.Join("\t", results.Names));
                 fileStream.WriteLine(String.Join("\t", results.Results));
             }
         }
         else if (IsFileLocked(fixedSettings.Storagefile))
         {
             Log.Information("[" + fixedSettings.Storagefile + "] File is busy, skipping saving of results");
         }
         else
         {
             Log.Information("[" + fixedSettings.Storagefile + "] Appending results to file");
             using (StreamWriter fileStream = new StreamWriter(fixedSettings.Storagefile, true))
             {
                 fileStream.WriteLine(String.Join("\t", results.Results));
             }
         }
     }
 }
示例#2
0
 //add log here
 public void Analyze(RawFileName rawfile, UIsettings fixedSettings, SettingsForAnalysis fixedSettingsForAnalysis, IProgress <DataRow> resultRow)
 {
     if (IsFileLocked(rawfile.FullName))
     {
         Log.Error("[" + rawfile.FullName + "] CRITICAL problem: file locked by another process! Skipping file");
     }
     else if (IsNotRawfile(rawfile.FullName))
     {
         Log.Error("[" + rawfile.FullName + "] CRITICAL problem: raw file corrupt! Skipping file");
     }
     else
     {
         Log.Information("[" + rawfile.FullName + "] Main analysis started");
         rawfile.SetCategories(fixedSettings.UserList, fixedSettings.LcList, fixedSettings.MsList, fixedSettings.SamplesList);
         SetRawFileHistory(rawfile, fixedSettings);//This is a mess with the class lines
         if (rawfile.SomethingWrongWithFileName)
         {
             Log.Warning("[" + rawfile.FullName + "] Please check file naming convention: parse rules and filename do not align.");
         }
         using (ResultItems results = new ResultItems())
         {
             Stopwatch stopwatch = new Stopwatch();
             stopwatch.Start();
             MainAnalysisThreadedTask(rawfile, fixedSettingsForAnalysis, fixedSettings, results);
             Log.Information("[" + rawfile.FullName + "] Main analysis finished in " + stopwatch.Elapsed.TotalMinutes.ToString("0.00") + " minutes");
             DoEmailResults(rawfile, fixedSettings, results);
             DoSqlUpdateResults(rawfile, fixedSettings, results);
             DoSaveResultsToFile(fixedSettings, results);
             AddResultRowToDataTable(results.Names, results.Results, results.Types, fixedSettings, resultRow);
         }
     }
 }
示例#3
0
        public List <Tuple <string, Type> > GetResultList(UIsettings settingName)
        {
            ResultItems results = GetResultItems(settingName);
            List <Tuple <string, Type> > nameType = new List <Tuple <string, Type> >();

            for (int i = 0; i < results.Count; i++)
            {
                nameType.Add(new Tuple <string, Type>(results.Names[i], results.Types[i]));
            }
            return(nameType);
        }
示例#4
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 public void Add(ResultItems newItems)
 {
     for (int i = 0; i < newItems.Names.Count; i++)
     {
         if (!resultDicIndex.ContainsKey(newItems.Names[i]))
         {
             resultDicIndex.Add(newItems.Names[i], Names.Count);
             Names.Add(newItems.Names[i]);
             Types.Add(newItems.Types[i]);
             Results.Add(newItems.Results[i]);
         }
     }
 }
示例#5
0
        private static void MainAnalysisThreadedTask(RawFileName rawfile, SettingsForAnalysis fixedSettingsForAnalysis, UIsettings fixedSettings, ResultItems results)
        {
            //ResultItems results = new ResultItems();

            //this can now be done threaded

            List <Task <ResultItems> > taskList = new List <Task <ResultItems> >();

            taskList.Add(Task.Run(() =>
            {
                ResultItems results1 = new ResultItems();
                using (AnalysisTemplate curMethod = new AnalysisMorpheus())
                {
                    results1 = curMethod.Analyze(rawfile, fixedSettingsForAnalysis, fixedSettings);
                }
                GC.Collect();//ugly but this solves problem with memory not released
                return(results1);
            }));
            taskList.Add(Task.Run(() =>
            {
                ResultItems results2 = new ResultItems();
                using (AnalysisTemplate curMethod = new AnalysisBase())
                {
                    results2 = curMethod.Analyze(rawfile, fixedSettingsForAnalysis, fixedSettings);
                }
                return(results2);
            }));
            taskList.Add(Task.Run(() =>
            {
                ResultItems results3 = new ResultItems();
                using (AnalysisTemplate curMethod = new AnalysisExternal1())
                {
                    results3 = curMethod.Analyze(rawfile, fixedSettingsForAnalysis, fixedSettings);
                }
                return(results3);
            }));

            Task.WaitAll(taskList.ToArray());
            foreach (Task <ResultItems> resultTask in taskList)
            {
                results.Add(resultTask.Result);
            }

            //return results;
        }
示例#6
0
        protected override ResultItems GetResultItems(UIsettings settingName)
        {
            ResultItems results = new ResultItems();

            foreach (ExternalResultParseSetting item in settingName.ExternalResults)
            {
                results.Add(item.Resultname, typeof(double));
            }

            /*
             * results.Add("MedianMS1IsolationInterference", typeof(double));
             * results.Add("MedianPeakWidthAt10Percent(s)", typeof(double));
             * results.Add("MedianPeakWidthAtHalfMax(s)", typeof(double));
             * results.Add("MedianAsymmetryFactor", typeof(double));
             * results.Add("ColumnCapacity", typeof(double));
             */
            return(results);
        }
示例#7
0
        protected override ResultItems GetResultItems(UIsettings settingName)
        {
            ResultItems results = new ResultItems();

            results.Add("RawFile", typeof(string));

            results.Add("User", typeof(string));
            results.Add("MS instrument", typeof(string));
            results.Add("MS instrument number", typeof(string));
            results.Add("LC instrument", typeof(string));
            results.Add("LC instrument number", typeof(string));
            results.Add("Sample type", typeof(string));
            results.Add("Sample type details", typeof(string));
            results.Add("File name convention followed", typeof(string));

            results.Add("LCMS start", typeof(DateTime));
            results.Add("MS start", typeof(DateTime));
            results.Add("LCMS end", typeof(DateTime));
            results.Add("MS time in minutes", typeof(double));
            results.Add("LC time in minutes", typeof(double));

            results.Add("File size (MiB)", typeof(double));
            results.Add("Storage space left (GiB)", typeof(double));

            results.Add("MS count", typeof(int));
            results.Add("MS2 count", typeof(int));
            results.Add("MS TIC", typeof(double));
            results.Add("MS TIC (high percentile)", typeof(double));
            results.Add("MS2 TIC", typeof(double));
            results.Add("MS signal to noise", typeof(double));
            results.Add("MS2 signal to noise", typeof(double));
            results.Add("MS ion count", typeof(double));
            results.Add("MS2 ion count", typeof(double));
            results.Add("MS2 topN", typeof(double));
            results.Add("Large injection time fluctuations", typeof(double));

            results.Add("CTCD or PrOSA minimum", typeof(double));
            results.Add("CTCD or PrOSA maximum", typeof(double));
            results.Add("Lock mass correction maximum absolute (ppm)", typeof(double));

            results.Add("MS2 count above ion threshold", typeof(int));
            results.Add("MS2 count above ion threshold percentage", typeof(double));
            results.Add("MS2 precursor isolation width TIC", typeof(double));
            results.Add("MS2TIC / MS2 precursor isolation width TIC", typeof(double));
            results.Add("MS2 scans with precursor as BP percentage", typeof(double));
            results.Add("MS2 scans XIC above precursor percentage", typeof(double));

            results.Add("MS2 with charge 2 in percent", typeof(double));
            results.Add("MS2 with charge 3 in percent", typeof(double));
            results.Add("MS2 with charge 4 or higher in percent", typeof(double));

            foreach (int day in new int[] { 1, 7, 30, 90 })
            {
                results.Add("Last " + day.ToString() + " day(s) LCMS usage percent", typeof(double));
                results.Add("Last " + day.ToString() + " day(s) MS usage percent", typeof(double));
                results.Add("Last " + day.ToString() + " day(s) MS excl QC usage percent", typeof(double));
            }

            results.Add("Polymer01", typeof(double));
            results.Add("Polymer02", typeof(double));
            results.Add("Polymer03", typeof(double));
            results.Add("Polymer04", typeof(double));
            results.Add("Polymer05", typeof(double));
            results.Add("AdductNa", typeof(double));
            results.Add("AdductCa", typeof(double));
            results.Add("AdductFe", typeof(double));
            results.Add("AdductK", typeof(double));
            results.Add("AdductFA", typeof(double));
            results.Add("AdductNH3", typeof(double));
            results.Add("AdductACN", typeof(double));
            results.Add("Precursor 5 percent mass quantile", typeof(double));
            results.Add("Precursor 95 percent mass quantile", typeof(double));
            results.Add("Warning log", typeof(string));
            results.Add("Analysis tool version", typeof(string));

            foreach (StatusLogItem item in settingName.statusLogItems)
            {
                if (item.CalculateMedian)
                {
                    results.Add(item.Name, typeof(double));
                }
                if (item.CalculateMin)
                {
                    results.Add(item.Name + " min", typeof(double));
                }
                if (item.CalculateMax)
                {
                    results.Add(item.Name + " max", typeof(double));
                }
                if (item.CalculateIQR)
                {
                    results.Add(item.Name + " IQR", typeof(double));
                }
            }

            return(results);
        }
示例#8
0
        public override ResultItems Analyze(RawFileName rawfile, SettingsForAnalysis settingName, UIsettings fixedSettings)
        {
            //Stopwatch stopwatch = new Stopwatch();
            //stopwatch.Start();
            ResultItems results = GetResultItems(fixedSettings);

            //MsScanParameters msScanParameters = new MsScanParameters(settingName);

            //progress.Report("[" + rawfile.FullName + "] Start at " + stopwatch.Elapsed.TotalMinutes.ToString("0.00") + " minutes");

            results.SetValue("RawFile", rawfile.BaseName);
            results.SetValue("User", rawfile.User);
            results.SetValue("MS instrument", rawfile.MsInstrument);
            results.SetValue("MS instrument number", rawfile.MsInstrumentDetails);
            results.SetValue("LC instrument", rawfile.LcInstrument);
            results.SetValue("LC instrument number", rawfile.LcInstrumentDetails);
            results.SetValue("Sample type", rawfile.SampleType);
            results.SetValue("Sample type details", rawfile.SampleTypeDetails);
            results.SetValue("File name convention followed", (!rawfile.SomethingWrongWithFileName).ToString()); // shitty hack, should be bool
            results.SetValue("File size (MiB)", rawfile.FileSizeMiB, 1);
            results.SetValue("Storage space left (GiB)", rawfile.SpaceLeftGiB, 1);

            if (settingName.UseBaseAnalysis)
            {
                StatusLog statusLog;
                using (RawFileProcessing rawfileResults = new RawFileProcessing(raw, rawfile.FullName, settingName))
                {
                    rawfile.SetDates(rawfileResults._filecreation, rawfileResults._msStart, rawfileResults._msEnd);
                    statusLog = rawfileResults.statusLog;
                    results.SetValue("Warning log", rawfileResults.WarningMessage);

                    results.SetValue("MS count", rawfileResults.MsCount, 0);
                    results.SetValue("MS TIC", rawfileResults.MsTic, 0);
                    results.SetValue("MS TIC (high percentile)", rawfileResults.MsTicHigh, 0);
                    results.SetValue("MS signal to noise", rawfileResults.MsS2N, 2);
                    results.SetValue("MS ion count", rawfileResults.MsIonCount, 0);

                    results.SetValue("CTCD or PrOSA minimum", rawfileResults.CtcdMin, 3);
                    results.SetValue("CTCD or PrOSA maximum", rawfileResults.CtcdMax, 3);
                    results.SetValue("Lock mass correction maximum absolute (ppm)", rawfileResults.LockMassCorrectionMaxAbsolute, 2);


                    results.SetValue("Large injection time fluctuations", rawfileResults.LargeFluctuations, 1); //set as parameter from usrcontrol
                    results.SetValue("Polymer01", rawfileResults.Polymer1, 1);
                    results.SetValue("Polymer02", rawfileResults.Polymer2, 1);
                    results.SetValue("Polymer03", rawfileResults.Polymer3, 1);
                    results.SetValue("Polymer04", rawfileResults.Polymer4, 1);
                    results.SetValue("Polymer05", rawfileResults.Polymer5, 1);
                    results.SetValue("AdductNa", rawfileResults.AdductNa, 1);
                    results.SetValue("AdductCa", rawfileResults.AdductCa, 1);
                    results.SetValue("AdductFe", rawfileResults.AdductFe, 1);
                    results.SetValue("AdductK", rawfileResults.AdductK, 1);
                    results.SetValue("AdductFA", rawfileResults.AdductFA, 1);
                    results.SetValue("AdductNH3", rawfileResults.AdductNH3, 1);
                    results.SetValue("AdductACN", rawfileResults.AdductACN, 1);
                    results.SetValue("Precursor 5 percent mass quantile", rawfileResults.PrecursorMass5percent, 1);
                    results.SetValue("Precursor 95 percent mass quantile", rawfileResults.PrecursorMass95percent, 1);
                    results.SetValue("MS2 topN", rawfileResults.TopN, 2);
                    results.SetValue("MS2 count", rawfileResults.Ms2Count, 0);
                    results.SetValue("MS2 TIC", rawfileResults.Ms2Tic, 0);
                    results.SetValue("MS2 signal to noise", rawfileResults.Ms2S2N, 2);
                    results.SetValue("MS2 ion count", rawfileResults.Ms2IonCount, 0);
                    results.SetValue("MS2 precursor isolation width TIC", rawfileResults.Ms2IsolationWindowTic, 0);
                    results.SetValue("MS2TIC / MS2 precursor isolation width TIC", rawfileResults.Ms2IsolationWindowTicRelative, 3);
                    results.SetValue("MS2 count above ion threshold", rawfileResults.Ms2ScansAboveIonThreshold, 0);
                    results.SetValue("MS2 with charge 2 in percent", rawfileResults.Ms2charge2, 2);
                    results.SetValue("MS2 with charge 3 in percent", rawfileResults.Ms2charge3, 2);
                    results.SetValue("MS2 with charge 4 or higher in percent", rawfileResults.Ms2charge4orMore, 2);
                    results.SetValue("MS2 scans XIC above precursor percentage", rawfileResults.Ms2ScansAbovePrecursorPercent, 2);
                    results.SetValue("MS2 count above ion threshold percentage", rawfileResults.Ms2ScansAboveIonThresholdPercent, 1);
                    results.SetValue("MS2 scans with precursor as BP percentage", rawfileResults.Ms2ScansWithPrecursorBasePeakPercent, 2);
                }

                results.SetValue("LCMS start", rawfile.GetDates(0));
                results.SetValue("MS start", rawfile.GetDates(1));
                results.SetValue("LCMS end", rawfile.GetDates(2));
                results.SetValue("MS time in minutes", rawfile.MsTime, 2);
                results.SetValue("LC time in minutes", rawfile.LcTime, 2);

                Dictionary <int, Tuple <double, double, double> > usage = rawfile.GetUsagePercent();
                foreach (int day in usage.Keys)
                {
                    results.SetValue("Last " + day.ToString() + " day(s) LCMS usage percent", usage[day].Item1, 1);
                    results.SetValue("Last " + day.ToString() + " day(s) MS usage percent", usage[day].Item2, 1);
                    results.SetValue("Last " + day.ToString() + " day(s) MS excl QC usage percent", usage[day].Item3, 1);
                }


                //status log entries

                foreach (StatusLogItem item in fixedSettings.statusLogItems)
                {
                    if (item.CalculateMedian)
                    {
                        results.SetValue(item.Name, statusLog.GetMedianOf(item.Name));
                    }
                    if (item.CalculateMin)
                    {
                        results.SetValue(item.Name + " min", statusLog.GetMinOf(item.Name));
                    }
                    if (item.CalculateMax)
                    {
                        results.SetValue(item.Name + " max", statusLog.GetMaxOf(item.Name));
                    }
                    if (item.CalculateIQR)
                    {
                        results.SetValue(item.Name + " IQR", statusLog.GetIqrOf(item.Name));
                    }
                }
            }

            results.SetValue("Analysis tool version", "0.0.1.21");
            return(results);
        }
示例#9
0
        public override ResultItems Analyze(RawFileName rawfile, SettingsForAnalysis settingName, UIsettings fixedSettings)
        {
            ResultItems   results    = GetResultItems(fixedSettings);
            List <double> resultlist = new List <double>();

            if (settingName.UseExternal1Analysis)
            {
                Log.Information("Started external1");
                string filename = rawfile.FullName;//"f:/temp2/20190114_QE99_Evo1_DBJ_E7_LFQprot_QC4_HELA_PAC_250ng_7500_01.raw";

                //get list of files and column/row names
                List <string> resultfiles = new List <string>();
                List <string> resultnames = new List <string>();
                foreach (ExternalResultParseSetting settings in fixedSettings.ExternalResults)
                {
                    string resultfile = settings.ResultFile;
                    resultfile = resultfile.Replace("{FILE}", rawfile.FullName);
                    resultfiles.Add(resultfile);
                    resultnames.Add(settings.Resultname);
                }


                //maybe add option to delete resultfile?
                try
                {
                    string arguments = fixedSettings.Arguments;
                    arguments  = arguments.Replace("{FILE}", rawfile.FullName);
                    resultlist = ExecuteProgram.GetResultsFromExternalProgram(
                        fixedSettings.Executable, //raw.exe
                        arguments,                //"parse -x -f " + filename
                        resultfiles.ToArray(),
                        resultnames.ToArray(),
                        fixedSettings.Timeout,
                        fixedSettings.ExternalToolSepChar,
                        !fixedSettings.AsRow);

                    if (resultlist.Count != fixedSettings.ExternalResults.Count)
                    {
                        resultlist.Clear();
                        for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
                        {
                            resultlist.Add(0.0);
                        }
                        Log.Error("External1 result was not parsed correctly (are headers correct?)");
                    }


                    Log.Information("Finished external1");
                }
                catch
                {
                    //something went wrong, adding 0s as filler and reporting error
                    Log.Error("External1 failed");
                    for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
                    {
                        resultlist.Add(0.0);
                    }
                }
            }
            else
            {
                //no analysis requested, adding 0s as filler
                for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
                {
                    resultlist.Add(0.0);
                }
            }
            //set results
            for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
            {
                results.SetValue(fixedSettings.ExternalResults[i].Resultname, resultlist[i]);
            }
            return(results);
        }
示例#10
0
 private static void DoEmailResults(RawFileName rawfile, UIsettings fixedSettings, ResultItems results)
 {
     if (fixedSettings.UseEmail)
     {
         using (EmailSystem emailSystem = new EmailSystem(fixedSettings.Mailserveradress, fixedSettings.Mailportname, fixedSettings.Mailusername, fixedSettings.Mailpassword))
         {
             if (emailSystem.Enabled)
             {
                 if (!emailSystem.CheckEmailAdress(rawfile.UserEmail, rawfile.User))
                 {
                     Log.Error("[" + rawfile.FullName + "] " + "Email can't be sent, email >" + rawfile.UserEmail + "< not correct for user: "******"");
                     string[]      compareSymbols = fixedSettings.CompareSymbols;
                     foreach (InformationKey ik in fixedSettings.informationKey)
                     {
                         bool addMessage;
                         if (ik.Message != "")
                         {
                             addMessage = CustomCompare(ik.Name, ik.ComparisonText1, results.Types[ik.ResultItemIndex1], results.Results[ik.ResultItemIndex1], compareSymbols[ik.ComparisonIndex1]);
                             addMessage = addMessage && CustomCompare(ik.Name, ik.ComparisonText2, results.Types[ik.ResultItemIndex2], results.Results[ik.ResultItemIndex2], compareSymbols[ik.ComparisonIndex2]);
                             addMessage = addMessage && CustomCompare(ik.Name, ik.ComparisonText3, results.Types[ik.ResultItemIndex3], results.Results[ik.ResultItemIndex3], compareSymbols[ik.ComparisonIndex3]);
                             addMessage = addMessage && CustomCompare(ik.Name, ik.ComparisonText4, results.Types[ik.ResultItemIndex4], results.Results[ik.ResultItemIndex4], compareSymbols[ik.ComparisonIndex4]);
                             addMessage = addMessage && CustomCompare(ik.Name, ik.ComparisonText5, results.Types[ik.ResultItemIndex5], results.Results[ik.ResultItemIndex5], compareSymbols[ik.ComparisonIndex5]);
                             if (addMessage)
                             {
                                 messageContent.Append(ik.Name);
                                 messageContent.Append(": ");
                                 messageContent.Append(ik.Message);
                                 messageContent.Append("<br />");
                             }
                         }
                     }
                     StringBuilder bodyContent = new StringBuilder("<table>");
                     for (int i = 0; i < results.Count; i++)
                     {
                         bodyContent.Append("<tr><td>");
                         bodyContent.Append(results.Names[i]);
                         bodyContent.Append("</td><td>");
                         bodyContent.Append(results.Results[i]);
                         bodyContent.Append("</td></tr>");
                     }
                     bodyContent.Append("</table>");
                     string mailresult = emailSystem.SendMail(rawfile.UserEmail, rawfile.User, rawfile.BaseName, bodyContent.ToString(), messageContent.ToString(), rawfile.CcEmails);
                     Log.Information("[" + rawfile.FullName + "] " + "UseEmail system reported " + mailresult);
                 }
             }
             else
             {
                 Log.Error("[" + rawfile.FullName + "] " + "UseEmail system couldn't initialize, is the server configured correctly?");
             }
         }
     }
 }
示例#11
0
 private static void DoSqlUpdateResults(RawFileName rawfile, UIsettings fixedSettings, ResultItems results)
 {
     if (fixedSettings.UseSql)
     {
         Log.Information("[" + rawfile.FullName + "] Uploading results to database");
         using (SQL newsql = new SQL(fixedSettings.Sqlserveradress, fixedSettings.Sqldatabase, fixedSettings.Sqltable, fixedSettings.Sqlusername, fixedSettings.Sqlpassword))
         {
             newsql.Insert(results.Names, results.ResultsWithMaxLength(255));
         }
     }
 }
示例#12
0
        protected virtual ResultItems GetResultItems(UIsettings settingName)
        {
            ResultItems results = new ResultItems();

            return(results);
        }