Exit codes for regular parsing

Exit code = number of errors (+ number of warnings, if warningsAreErrors = true)
Works for regular;
TODO: implement for xic and query

Author: caetera

MainClass.cs

@@ -447,6 +447,10 @@ private static void RegularParametersParsing(string[] args)
                     "N|noiseData", "Include noise data in mzML output",
                     v => parseInput.NoiseData = v != null
                 },
+                {
+                  "w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
+                    v => parseInput.Vigilant = v != null 
+                },
                 {
                     "u:|s3_url:",
                     "Optional property to write directly the data into S3 Storage.",
@@ -677,7 +681,9 @@ private static void RegularParametersParsing(string[] args)
 
                 RawFileParser.Parse(parseInput);
 
-                exitCode = 0;
+                Log.Info($"Processing completed {parseInput.Errors} errors, {parseInput.Warnings} warnings");
+
+                exitCode = parseInput.Vigilant ? parseInput.Errors + parseInput.Warnings: parseInput.Errors;
             }
             catch (UnauthorizedAccessException ex)
             {

ParseInput.cs

@@ -14,6 +14,10 @@ public class ParseInput
         /// </summary>
         private string _rawFilePath;
 
+        private int _errors;
+
+        private int _warnings;
+
         /// <summary>
         /// The RAW folder path.
         /// </summary>
@@ -32,6 +36,15 @@ public string RawFilePath
             }
         }
 
+        public int Errors
+        {
+            get => _errors;
+        }
+        public int Warnings
+        {
+            get => _warnings;
+        }
+
         /// <summary>
         /// The output directory.
         /// </summary>
@@ -82,6 +95,8 @@ public string RawFilePath
 
         public bool StdOut { get; set; }
 
+        public bool Vigilant { get; set; }
+
         private S3Loader S3Loader { get; set; }
 
         public string S3AccessKeyId { get; set; }
@@ -111,6 +126,9 @@ public ParseInput()
             MgfPrecursor = false;
             StdOut = false;
             NoiseData = false;
+            Vigilant = false;
+            _errors = 0;
+            _warnings = 0;
         }
 
         public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat
@@ -127,5 +145,15 @@ public void InitializeS3Bucket()
         {
             S3Loader = new S3Loader(S3Url, S3AccessKeyId, S3SecretAccessKey, BucketName);
         }
+
+        public void NewError()
+        {
+            _errors++;
+        }
+
+        public void NewWarn()
+        {
+            _warnings++;
+        }
     }
 }

RawFileParser.cs

@@ -61,22 +61,26 @@ private static void TryProcessFile(ParseInput parseInput)
             {
                 ProcessFile(parseInput);
             }
-            catch (UnauthorizedAccessException ex)
-            {
-                Log.Error(!ex.Message.IsNullOrEmpty()
-                    ? ex.Message
-                    : "Attempting to write to an unauthorized location.");
-            }
+            
             catch (Exception ex)
             {
-                if (ex is RawFileParserException)
+                if (ex is UnauthorizedAccessException)
+                {
+                    Log.Error(!ex.Message.IsNullOrEmpty()
+                        ? ex.Message
+                        : "Attempting to write to an unauthorized location.");
+                    parseInput.NewError();
+                }
+                else if (ex is RawFileParserException)
                 {
                     Log.Error(ex.Message);
+                    parseInput.NewError();
                 }
                 else
                 {
-                    Log.Error("An unexpected error occured while parsing file:" + parseInput.RawFilePath);
+                    Log.Error("An unexpected error occured (see below)");
                     Log.Error(ex.ToString());
+                    parseInput.NewError();
                 }
             }
         }

Writer/MgfSpectrumWriter.cs

@@ -83,6 +83,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                     catch (Exception ex)
                     {
                         Log.WarnFormat("Cannot load trailer infromation for scan {0} due to following exception\n{1}", scanNumber, ex.Message);
+                        ParseInput.NewWarn();
                         trailerData = new ScanTrailer();
                     }
 
@@ -141,9 +142,14 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                             }
 
                             if (_precursorScanNumber > 0)
+                            {
                                 precursorReference = ConstructSpectrumTitle((int)Device.MS, 1, _precursorScanNumber);
+                            }
                             else
+                            {
                                 Log.Error($"Failed finding precursor for {scanNumber}");
+                                ParseInput.NewError();
+                            }
                         }
                     }
 

Writer/MzMlSpectrumWriter.cs

@@ -591,6 +591,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                     catch (Exception ex)
                     {
                         Log.Error(ex);
+                        ParseInput.NewError();
                     }
                 }
 
@@ -665,16 +666,17 @@ private void PopulateInstrumentConfigurationList(int firstScanNumber, int lastSc
                                 OntologyMapping.IonizationTypes[scanFilter.IonizationMode]);
                         }
                     }
-                    catch (Exception e)
+                    catch (Exception)
                     {
                         if (!ParseInput.IgnoreInstrumentErrors)
                         {
-                            Log.ErrorFormat("Unsupported Ionization Mode - {0}; Use ignoreInstrumentErrors key to suppress this error", scanFilter.IonizationMode.ToString());
-                            throw e;
+                            Log.ErrorFormat("Unsupported ionization mode - {0}; Use ignoreInstrumentErrors key to suppress this error", scanFilter.IonizationMode.ToString());
+                            throw;
                         }
                         else
                         {
                             Log.WarnFormat("Unsupported Ionization Mode - {0}", scanFilter.IonizationMode.ToString());
+                            ParseInput.NewWarn();
                         }
                     }
 
@@ -694,12 +696,13 @@ private void PopulateInstrumentConfigurationList(int firstScanNumber, int lastSc
                 {
                     if (!ParseInput.IgnoreInstrumentErrors)
                     {
-                        Log.ErrorFormat("No Scan Filter found for the following scan {0}; Use ignoreInstrumentErrors key to suppress", scanNumber);
+                        Log.ErrorFormat("No scan filter found for the following scan {0}; Use ignoreInstrumentErrors key to suppress", scanNumber);
                         throw;
                     }
                     else
                     {
                         Log.WarnFormat("No Scan Filter found for the following scan {0}", scanNumber);
+                        ParseInput.NewWarn();
                     }
                 }
 
@@ -1201,6 +1204,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             catch (Exception ex)
             {
                 Log.WarnFormat("Cannot load trailer infromation for scan {0} due to following exception\n{1}", scanNumber, ex.Message);
+                ParseInput.NewWarn();
                 trailerData = new ScanTrailer();
             }
 
@@ -1325,6 +1329,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                     };
 
                     Log.Error($"Failed finding precursor for {scanNumber}");
+                    ParseInput.NewError();
                 }
             }
             else
@@ -2129,6 +2134,7 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
             catch (ArgumentOutOfRangeException)
             {
                 Log.Warn($"Failed to get reaction when parsing precursor {precursorScanNumber}");
+                ParseInput.NewWarn();
             }
 
             var precursor = new PrecursorType
@@ -2315,6 +2321,7 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
 
                             default:
                                 Log.Warn($"Unknown supplemental activation type: {reaction.ActivationType}");
+                                ParseInput.NewWarn();
                                 break;
 
                         }