Refine messages

caetera · caetera · commit f5bbd4c215ea · 2022-10-21T17:28:57.000+02:00
diff --git a/Query/ProxiSpectrumReader.cs b/Query/ProxiSpectrumReader.cs
@@ -28,6 +28,8 @@ public List<ProxiSpectrum> Retrieve()
             IRawDataPlus rawFile;
             using (rawFile = RawFileReaderFactory.ReadFile(queryParameters.rawFilePath))
             {
+                Log.Info($"Started parsing {queryParameters.rawFilePath}");
+
                 if (!rawFile.IsOpen)
                 {
                     throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");
@@ -37,13 +39,13 @@ public List<ProxiSpectrum> Retrieve()
                 if (rawFile.IsError)
                 {
                     throw new RawFileParserException(
-                        $"Error opening ({rawFile.FileError}) - {queryParameters.rawFilePath}");
+                        $"RAW file cannot be processed because of an error - {rawFile.FileError}");
                 }
 
                 // Check if the RAW file is being acquired
                 if (rawFile.InAcquisition)
                 {
-                    throw new RawFileParserException("RAW file still being acquired - " + queryParameters.rawFilePath);
+                    throw new RawFileParserException("RAW file cannot be processed since it is still being acquired");
                 }
 
                 // Get the number of instruments (controllers) present in the RAW file and set the 
@@ -227,7 +229,7 @@ public List<ProxiSpectrum> Retrieve()
                     {
                         if (ex.GetBaseException() is IndexOutOfRangeException)
                         {
-                            Log.WarnFormat("Spectrum #{0} outside of file boundries", scanNumber);
+                            Log.WarnFormat("Spectrum #{0} is outside of file boundries", scanNumber);
                             queryParameters.NewWarn();
                         }
                         else
@@ -238,6 +240,8 @@ public List<ProxiSpectrum> Retrieve()
                 }
             }
 
+            Log.Info($"Finished processing {queryParameters.rawFilePath}");
+
             return resultList;
         }
     }
diff --git a/RawFileParser.cs b/RawFileParser.cs
@@ -103,13 +103,13 @@ private static void ProcessFile(ParseInput parseInput)
                 // Check for any errors in the RAW file
                 if (rawFile.IsError)
                 {
-                    throw new RawFileParserException($"Error opening ({rawFile.FileError}) - {parseInput.RawFilePath}");
+                    throw new RawFileParserException($"RAW file cannot be processed because of an error - {rawFile.FileError}");
                 }
 
                 // Check if the RAW file is being acquired
                 if (rawFile.InAcquisition)
                 {
-                    throw new RawFileParserException("RAW file still being acquired - " + parseInput.RawFilePath);
+                    throw new RawFileParserException("RAW file cannot be processed since it is still being acquired");
                 }
 
                 // Get the number of instruments (controllers) present in the RAW file and set the 
diff --git a/Writer/MetadataWriter.cs b/Writer/MetadataWriter.cs
@@ -93,6 +93,7 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
                         catch (ArgumentOutOfRangeException)
                         {
                             Log.Warn("No reaction found for scan " + scanNumber);
+                            _parseInput.NewWarn();
                         }
 
                         // trailer extra data list
diff --git a/Writer/MgfSpectrumWriter.cs b/Writer/MgfSpectrumWriter.cs
@@ -242,7 +242,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
 
                         Writer.WriteLine("END IONS");
 
-                        Log.Debug("Spectrum written to file -- SCAN " + scanNumber);
+                        Log.Debug("Spectrum written to file -- SCAN# " + scanNumber);
                     }
                 }
 
diff --git a/Writer/MzMlSpectrumWriter.cs b/Writer/MzMlSpectrumWriter.cs
@@ -1362,7 +1362,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                 case PolarityType.Any:
                     break;
                 default:
-                    throw new ArgumentOutOfRangeException();
+                    throw new ArgumentOutOfRangeException("PolarityType is Unknown");
             }
 
             // Total ion current
diff --git a/XIC/XicExecutor.cs b/XIC/XicExecutor.cs
@@ -55,7 +55,7 @@ public static void Run(XicParameters parameters)
                         directory = Path.GetDirectoryName(rawFile);
                     }
 
-                    var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException(),
+                    var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException("Output directory cannot be null"),
                         Path.GetFileNameWithoutExtension(rawFile) + ".json");
 
                     OutputXicData(dataInstance, outputFileName);
diff --git a/XIC/XicReader.cs b/XIC/XicReader.cs
@@ -21,6 +21,8 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref
             IRawDataPlus rawFile;
             using (rawFile = RawFileReaderFactory.ReadFile(rawFilePath))
             {
+                Log.Info($"Started parsing {rawFilePath}");
+
                 if (!rawFile.IsOpen)
                 {
                     throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");
@@ -30,13 +32,13 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref
                 if (rawFile.IsError)
                 {
                     throw new RawFileParserException(
-                        $"Error opening ({rawFile.FileError}) - {rawFilePath}");
+                        $"RAW file cannot be processed because of an error - {rawFile.FileError}");
                 }
 
                 // Check if the RAW file is being acquired
                 if (rawFile.InAcquisition)
                 {
-                    throw new RawFileParserException("RAW file still being acquired - " + rawFilePath);
+                    throw new RawFileParserException("RAW file cannot be processed since it is still being acquired");
                 }
 
                 // Get the number of instruments (controllers) present in the RAW file and set the 
@@ -124,14 +126,14 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref
                                  Math.Abs(data.PositionsArray[0][0] - endTime) < 0.001))
                             {
                                 Log.Warn(
-                                    $"Only the minimum or maximum retention time was returned. This is an indication that the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]");
+                                    $"Only the minimum or maximum retention time was returned. Does the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]?");
                                 parameters.NewWarn();
                             }
                         }
                         else
                         {
                             Log.Warn(
-                                $"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. This is an indication that the provided retention time window lies outside the max. window [{startTime}-{endTime}]");
+                                $"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. Does the provided retention time window lies outside the max. window [{startTime}-{endTime}]");
                             parameters.NewWarn();
                         }
                     }
@@ -172,6 +174,8 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref
                         }
                     }
                 }
+
+                Log.Info($"Finished parsing {rawFilePath}");
             }
         }
 

Original file line number	Diff line number	Diff line change
`@@ -28,6 +28,8 @@ public List<ProxiSpectrum> Retrieve()`
`28`	`28`	`IRawDataPlus rawFile;`
`29`	`29`	`using (rawFile = RawFileReaderFactory.ReadFile(queryParameters.rawFilePath))`
`30`	`30`	`{`
	`31`	`+ Log.Info($"Started parsing {queryParameters.rawFilePath}");`
	`32`	`+`
`31`	`33`	`if (!rawFile.IsOpen)`
`32`	`34`	`{`
`33`	`35`	`throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");`
`@@ -37,13 +39,13 @@ public List<ProxiSpectrum> Retrieve()`
`37`	`39`	`if (rawFile.IsError)`
`38`	`40`	`{`
`39`	`41`	`throw new RawFileParserException(`
`40`		`- $"Error opening ({rawFile.FileError}) - {queryParameters.rawFilePath}");`
	`42`	`+ $"RAW file cannot be processed because of an error - {rawFile.FileError}");`
`41`	`43`	`}`
`42`	`44`
`43`	`45`	`// Check if the RAW file is being acquired`
`44`	`46`	`if (rawFile.InAcquisition)`
`45`	`47`	`{`
`46`		`- throw new RawFileParserException("RAW file still being acquired - " + queryParameters.rawFilePath);`
	`48`	`+ throw new RawFileParserException("RAW file cannot be processed since it is still being acquired");`
`47`	`49`	`}`
`48`	`50`
`49`	`51`	`// Get the number of instruments (controllers) present in the RAW file and set the`
`@@ -227,7 +229,7 @@ public List<ProxiSpectrum> Retrieve()`
`227`	`229`	`{`
`228`	`230`	`if (ex.GetBaseException() is IndexOutOfRangeException)`
`229`	`231`	`{`
`230`		`- Log.WarnFormat("Spectrum #{0} outside of file boundries", scanNumber);`
	`232`	`+ Log.WarnFormat("Spectrum #{0} is outside of file boundries", scanNumber);`
`231`	`233`	`queryParameters.NewWarn();`
`232`	`234`	`}`
`233`	`235`	`else`
`@@ -238,6 +240,8 @@ public List<ProxiSpectrum> Retrieve()`
`238`	`240`	`}`
`239`	`241`	`}`
`240`	`242`
	`243`	`+ Log.Info($"Finished processing {queryParameters.rawFilePath}");`
	`244`	`+`
`241`	`245`	`return resultList;`
`242`	`246`	`}`
`243`	`247`	`}`
Original file line number	Diff line number	Diff line change
`@@ -103,13 +103,13 @@ private static void ProcessFile(ParseInput parseInput)`
`103`	`103`	`// Check for any errors in the RAW file`
`104`	`104`	`if (rawFile.IsError)`
`105`	`105`	`{`
`106`		`- throw new RawFileParserException($"Error opening ({rawFile.FileError}) - {parseInput.RawFilePath}");`
	`106`	`+ throw new RawFileParserException($"RAW file cannot be processed because of an error - {rawFile.FileError}");`
`107`	`107`	`}`
`108`	`108`
`109`	`109`	`// Check if the RAW file is being acquired`
`110`	`110`	`if (rawFile.InAcquisition)`
`111`	`111`	`{`
`112`		`- throw new RawFileParserException("RAW file still being acquired - " + parseInput.RawFilePath);`
	`112`	`+ throw new RawFileParserException("RAW file cannot be processed since it is still being acquired");`
`113`	`113`	`}`
`114`	`114`
`115`	`115`	`// Get the number of instruments (controllers) present in the RAW file and set the`
Original file line number	Diff line number	Diff line change
`@@ -93,6 +93,7 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca`
`93`	`93`	`catch (ArgumentOutOfRangeException)`
`94`	`94`	`{`
`95`	`95`	`Log.Warn("No reaction found for scan " + scanNumber);`
	`96`	`+ _parseInput.NewWarn();`
`96`	`97`	`}`
`97`	`98`
`98`	`99`	`// trailer extra data list`
Original file line number	Diff line number	Diff line change
`@@ -242,7 +242,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc`
`242`	`242`
`243`	`243`	`Writer.WriteLine("END IONS");`
`244`	`244`
`245`		`- Log.Debug("Spectrum written to file -- SCAN " + scanNumber);`
	`245`	`+ Log.Debug("Spectrum written to file -- SCAN# " + scanNumber);`
`246`	`246`	`}`
`247`	`247`	`}`
`248`	`248`
Original file line number	Diff line number	Diff line change
`@@ -1362,7 +1362,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)`
`1362`	`1362`	`case PolarityType.Any:`
`1363`	`1363`	`break;`
`1364`	`1364`	`default:`
`1365`		`- throw new ArgumentOutOfRangeException();`
	`1365`	`+ throw new ArgumentOutOfRangeException("PolarityType is Unknown");`
`1366`	`1366`	`}`
`1367`	`1367`
`1368`	`1368`	`// Total ion current`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ public static void Run(XicParameters parameters)`
`55`	`55`	`directory = Path.GetDirectoryName(rawFile);`
`56`	`56`	`}`
`57`	`57`
`58`		`- var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException(),`
	`58`	`+ var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException("Output directory cannot be null"),`
`59`	`59`	`Path.GetFileNameWithoutExtension(rawFile) + ".json");`
`60`	`60`
`61`	`61`	`OutputXicData(dataInstance, outputFileName);`
Original file line number	Diff line number	Diff line change
`@@ -21,6 +21,8 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref`
`21`	`21`	`IRawDataPlus rawFile;`
`22`	`22`	`using (rawFile = RawFileReaderFactory.ReadFile(rawFilePath))`
`23`	`23`	`{`
	`24`	`+ Log.Info($"Started parsing {rawFilePath}");`
	`25`	`+`
`24`	`26`	`if (!rawFile.IsOpen)`
`25`	`27`	`{`
`26`	`28`	`throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");`
`@@ -30,13 +32,13 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref`
`30`	`32`	`if (rawFile.IsError)`
`31`	`33`	`{`
`32`	`34`	`throw new RawFileParserException(`
`33`		`- $"Error opening ({rawFile.FileError}) - {rawFilePath}");`
	`35`	`+ $"RAW file cannot be processed because of an error - {rawFile.FileError}");`
`34`	`36`	`}`
`35`	`37`
`36`	`38`	`// Check if the RAW file is being acquired`
`37`	`39`	`if (rawFile.InAcquisition)`
`38`	`40`	`{`
`39`		`- throw new RawFileParserException("RAW file still being acquired - " + rawFilePath);`
	`41`	`+ throw new RawFileParserException("RAW file cannot be processed since it is still being acquired");`
`40`	`42`	`}`
`41`	`43`
`42`	`44`	`// Get the number of instruments (controllers) present in the RAW file and set the`
`@@ -124,14 +126,14 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref`
`124`	`126`	`Math.Abs(data.PositionsArray[0][0] - endTime) < 0.001))`
`125`	`127`	`{`
`126`	`128`	`Log.Warn(`
`127`		`- $"Only the minimum or maximum retention time was returned. This is an indication that the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]");`
	`129`	`+ $"Only the minimum or maximum retention time was returned. Does the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]?");`
`128`	`130`	`parameters.NewWarn();`
`129`	`131`	`}`
`130`	`132`	`}`
`131`	`133`	`else`
`132`	`134`	`{`
`133`	`135`	`Log.Warn(`
`134`		`- $"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. This is an indication that the provided retention time window lies outside the max. window [{startTime}-{endTime}]");`
	`136`	`+ $"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. Does the provided retention time window lies outside the max. window [{startTime}-{endTime}]");`
`135`	`137`	`parameters.NewWarn();`
`136`	`138`	`}`
`137`	`139`	`}`
`@@ -172,6 +174,8 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData, ref`
`172`	`174`	`}`
`173`	`175`	`}`
`174`	`176`	`}`
	`177`	`+`
	`178`	`+ Log.Info($"Finished parsing {rawFilePath}");`
`175`	`179`	`}`
`176`	`180`	`}`
`177`	`181`