Added additional bad inputs and enhanced error handling.

.gitattributes

@@ -6,4 +6,7 @@
 
 # Denote all files that are truly binary and should not be modified.
 *.png binary
-*.jpg binary
+*.jpg binary
+
+# Treat these files as text so we don;t get inconsistency with line endings between OS
+tests/NHapi.NUnit/TestData/BadInputs/**/*   -text

src/NHapi.Base/Model/AbstractGroup.cs

@@ -537,7 +537,7 @@ private IStructure TryToInstantiateStructure(Type c, string name)
                     if (!(o is IStructure))
                     {
                         throw new HL7Exception(
-                            $"Class {c.FullName} does not implement ca.on.uhn.hl7.message.Structure",
+                            $"Class {c.FullName} does not implement IStructure",
                             ErrorCode.APPLICATION_INTERNAL_ERROR);
                     }
 
@@ -546,12 +546,10 @@ private IStructure TryToInstantiateStructure(Type c, string name)
             }
             catch (Exception e)
             {
-                if (e is HL7Exception)
-                {
-                    throw (HL7Exception)e;
-                }
-
-                throw new HL7Exception($"Can't instantiate class {c.FullName}", ErrorCode.APPLICATION_INTERNAL_ERROR, e);
+                throw new HL7Exception(
+                    $"Can't instantiate class {c.FullName}",
+                    ErrorCode.APPLICATION_INTERNAL_ERROR,
+                    e);
             }
 
             return s;
@@ -572,7 +570,7 @@ private string GetStructureName(Type c)
             if (typeof(IGroup).IsAssignableFrom(c) && !typeof(IMessage).IsAssignableFrom(c))
             {
                 var messageName = Message.GetStructureName();
-                if (name.StartsWith(messageName) && name.Length > messageName.Length)
+                if (name.StartsWith(messageName, StringComparison.Ordinal) && name.Length > messageName.Length)
                 {
                     name = name.Substring(messageName.Length + 1);
                 }

src/NHapi.Base/PackageManager.cs

@@ -69,6 +69,11 @@ public IList<Hl7Package> GetAllPackages()
 
         public bool IsValidVersion(string version)
         {
+            if (version == null)
+            {
+                return false;
+            }
+
             version = version.ToUpper().Trim();
             foreach (var package in Packages)
             {

src/NHapi.Base/Parser/EncodingDetector.cs

@@ -53,7 +53,7 @@ public static void AssertEr7Encoded(string message)
             }
 
             // string should start with "MSH"
-            if (!message.StartsWith("MSH"))
+            if (!message.StartsWith("MSH", StringComparison.Ordinal))
             {
                 throw new ArgumentException("The message does not start with MSH");
             }

src/NHapi.Base/Parser/Escape.cs

@@ -295,17 +295,18 @@ private void BuildLookups(EncodingCharacters encoding)
 
                 for (var i = 0; i < Codes.Length; i++)
                 {
+                    var key = SpecialCharacters[i];
                     var seq = $"{encoding.EscapeCharacter}{Codes[i]}{encoding.EscapeCharacter}";
 
-                    EscapeSequences.Add(SpecialCharacters[i], seq);
+                    TryAddEscapeSequence(key, seq);
                 }
 
                 // Escaping of truncation # is not implemented yet. It may only be escaped if it is the first character that
                 // exceeds the conformance length of the component (ch 2.5.5.2). As of now, this information is not
                 // available at this place.
-                EscapeSequences.Add(TruncateChar, $"{TruncateChar}");
-                EscapeSequences.Add(LineFeed, $"\\{LineFeedHexadecimal}\\");
-                EscapeSequences.Add(CarriageReturn, $"\\{CarriageReturnHexadecimal}\\");
+                TryAddEscapeSequence(TruncateChar, $"{TruncateChar}");
+                TryAddEscapeSequence(LineFeed, $"\\{LineFeedHexadecimal}\\");
+                TryAddEscapeSequence(CarriageReturn, $"\\{CarriageReturnHexadecimal}\\");
             }
 
             private void LoadHexadecimalConfiguration()
@@ -317,6 +318,14 @@ private void LoadHexadecimalConfiguration()
                     CarriageReturnHexadecimal = configSection.HexadecimalEscaping.CarriageReturnHexadecimal;
                 }
             }
+
+            private void TryAddEscapeSequence(char key, string value)
+            {
+                if (!EscapeSequences.ContainsKey(key))
+                {
+                    EscapeSequences.Add(key, value);
+                }
+            }
         }
     }
 }

src/NHapi.Base/Parser/LegacyPipeParser.cs

@@ -327,7 +327,7 @@ public override string GetEncoding(string message)
             var ok = true;
 
             // string should start with "MSH"
-            if (!message.StartsWith("MSH"))
+            if (!message.StartsWith("MSH", StringComparison.Ordinal))
             {
                 return null;
             }
@@ -620,21 +620,23 @@ public override string GetVersion(string message)
                     ErrorCode.REQUIRED_FIELD_MISSING);
             }
 
-            string version;
-            if (fields.Length >= 12)
+            if (fields.Length < 12)
             {
-                if (fields[11] == null)
-                {
-                    throw new HL7Exception("MSH Version field is null.", ErrorCode.REQUIRED_FIELD_MISSING);
-                }
+                throw new HL7Exception(
+                    $"Can't find version ID - MSH has only {fields.Length} fields.",
+                    ErrorCode.REQUIRED_FIELD_MISSING);
+            }
 
-                version = Split(fields[11], compSep)[0];
+            if (fields[11] == null)
+            {
+                throw new HL7Exception("MSH Version field is null.", ErrorCode.REQUIRED_FIELD_MISSING);
             }
-            else
+
+            var version = Split(fields[11], compSep)[0];
+
+            if (version == null)
             {
-                throw new HL7Exception(
-                    "Can't find version ID - MSH has only " + fields.Length + " fields.",
-                    ErrorCode.REQUIRED_FIELD_MISSING);
+                throw new HL7Exception("MSH Version field is invalid.", ErrorCode.REQUIRED_FIELD_MISSING);
             }
 
             return version.Trim();

src/NHapi.Base/Parser/MessageIterator.cs

@@ -117,7 +117,7 @@ public virtual bool MoveNext()
 
                 var structureDefinition = currentPosition.StructureDefinition;
 
-                if (structureDefinition.IsSegment && structureDefinition.Name.StartsWith(direction) && (structureDefinition.IsRepeating || currentPosition.Repetition == -1))
+                if (structureDefinition.IsSegment && structureDefinition.Name.StartsWith(direction, StringComparison.Ordinal) && (structureDefinition.IsRepeating || currentPosition.Repetition == -1))
                 {
                     nextIsSet = true;
                     currentPosition.IncrementRepetition();
@@ -224,29 +224,31 @@ private void AddNonStandardSegmentAtCurrentPosition()
             // Check if the structure already has a non-standard segment in the appropriate
             // position
             var currentNames = parentStructure.Names;
-            if (index < currentNames.Length && currentNames[index].StartsWith(direction))
+            if (index < currentNames.Length && currentNames[index].StartsWith(direction, StringComparison.Ordinal))
             {
                 newSegmentName = currentNames[index];
             }
             else
             {
-                try
-                {
-                    newSegmentName = parentStructure.AddNonstandardSegment(direction, index);
-                }
-                catch (HL7Exception e)
-                {
-                    throw new InvalidOperationException($"Unable to add nonstandard segment {direction}: ", e);
-                }
+                newSegmentName = parentStructure.AddNonstandardSegment(direction, index);
             }
 
-            var previousSibling = GetCurrentPosition().StructureDefinition;
-            var parentStructureDefinition = parentDefinitionPath.Last().StructureDefinition;
-            var nextDefinition = new NonStandardStructureDefinition(parentStructureDefinition, previousSibling, newSegmentName, index);
-            currentDefinitionPath = parentDefinitionPath;
-            currentDefinitionPath.Add(new Position(nextDefinition, 0));
+            try
+            {
+                var previousSibling = GetCurrentPosition().StructureDefinition;
+                var parentStructureDefinition = parentDefinitionPath.Last().StructureDefinition;
+                var nextDefinition = new NonStandardStructureDefinition(parentStructureDefinition, previousSibling, newSegmentName, index);
+                currentDefinitionPath = parentDefinitionPath;
+                currentDefinitionPath.Add(new Position(nextDefinition, 0));
 
-            nextIsSet = true;
+                nextIsSet = true;
+            }
+            catch (Exception ex)
+            {
+                throw new HL7Exception(
+                    $"Could not add non-standard segment at current position.",
+                    ex);
+            }
         }
 
         private IStructure NavigateToStructure(IEnumerable<Position> theDefinitionPath)
@@ -260,17 +262,10 @@ private IStructure NavigateToStructure(IEnumerable<Position> theDefinitionPath)
                 }
                 else
                 {
-                    try
-                    {
-                        var structureDefinition = next.StructureDefinition;
-                        var currentStructureGroup = (IGroup)currentStructure;
-                        var nextStructureName = structureDefinition.NameAsItAppearsInParent;
-                        currentStructure = currentStructureGroup.GetStructure(nextStructureName, next.Repetition);
-                    }
-                    catch (HL7Exception e)
-                    {
-                        throw new InvalidOperationException("Failed to retrieve structure: ", e);
-                    }
+                    var structureDefinition = next.StructureDefinition;
+                    var currentStructureGroup = (IGroup)currentStructure;
+                    var nextStructureName = structureDefinition.NameAsItAppearsInParent;
+                    currentStructure = currentStructureGroup.GetStructure(nextStructureName, next.Repetition);
                 }
             }
 
@@ -283,6 +278,12 @@ private List<Position> PopUntilMatchFound(List<Position> theDefinitionPath)
             {
                 theDefinitionPath = new List<Position>(theDefinitionPath.GetRange(0, theDefinitionPath.Count - 1));
 
+                if (theDefinitionPath.Count == 0)
+                {
+                    Log.Debug($"The created list of positions contains no elements.");
+                    return null;
+                }
+
                 var newCurrentPosition = theDefinitionPath.Last();
                 var newCurrentStructureDefinition = newCurrentPosition.StructureDefinition;
 

src/NHapi.Base/Parser/ParserBase.cs

@@ -199,7 +199,7 @@ public virtual IMessage Parse(string message)
             if (!SupportsEncoding(encoding))
             {
                 string startOfMessage = null;
-                if (message.StartsWith("MSH"))
+                if (message.StartsWith("MSH", StringComparison.Ordinal))
                 {
                     var indexOfCarriageReturn = message.IndexOf('\r');
                     if (indexOfCarriageReturn > 0)
@@ -421,10 +421,24 @@ public bool SupportsEncoding(string encoding)
         /// <exception cref="HL7Exception">Thrown when the version is not recognized or no appropriate class can be found or the Message.</exception>
         protected internal virtual IMessage InstantiateMessage(string theName, string theVersion, bool isExplicit)
         {
-            var messageClass = Factory.GetMessageClass(theName, theVersion, isExplicit);
+            Type messageClass;
+            try
+            {
+                messageClass = Factory.GetMessageClass(theName, theVersion, isExplicit);
+            }
+            catch (Exception ex)
+            {
+                throw new HL7Exception(
+                    $"Can't find message class in current package list: {theName}",
+                    ErrorCode.UNSUPPORTED_MESSAGE_TYPE,
+                    ex);
+            }
+
             if (messageClass == null)
             {
-                throw new HL7Exception($"Can't find message class in current package list: {theName}", ErrorCode.UNSUPPORTED_MESSAGE_TYPE);
+                throw new HL7Exception(
+                    $"Can't find message class in current package list: {theName}",
+                    ErrorCode.UNSUPPORTED_MESSAGE_TYPE);
             }
 
             Log.Info($"Instantiating msg of class {messageClass.FullName}");

src/NHapi.Base/Parser/PipeParser.cs

@@ -467,7 +467,13 @@ public override void Parse(IMessage message, string @string)
 
                     if (messageIterator.MoveNext())
                     {
-                        var next = (ISegment)messageIterator.Current;
+                        var next = messageIterator.Current as ISegment;
+
+                        if (next == null)
+                        {
+                            throw new HL7Exception($"Current segment does not implement ISegment and therefore cannot be parsed.");
+                        }
+
                         Parse(next, segments[i], GetEncodingChars(@string), repetition);
                     }
                 }
@@ -602,7 +608,7 @@ public override string GetVersion(string message)
             var fields = Split(msh, fieldSep);
 
             string compSep;
-            if (fields.Length >= 2 && (fields[1].Length == 4 || fields[1].Length == 5))
+            if (fields.Length >= 2 && (fields[1]?.Length == 4 || fields[1]?.Length == 5))
             {
                 compSep = Convert.ToString(fields[1][0]); // get component separator as 1st encoding char
             }
@@ -613,29 +619,22 @@ public override string GetVersion(string message)
                     ErrorCode.REQUIRED_FIELD_MISSING);
             }
 
-            string version;
-            if (fields.Length >= 12)
+            if (fields.Length < 12)
             {
-                var comp = Split(fields[11], compSep);
-                if (comp.Length >= 1)
-                {
-                    version = comp[0];
-                }
-                else
-                {
-                    throw new HL7Exception(
-                        $"Can't find version ID - MSH.12 is {fields[11]}",
-                        ErrorCode.REQUIRED_FIELD_MISSING);
-                }
+                throw new HL7Exception(
+                    $"Can't find version ID - MSH has only {fields.Length} fields.",
+                    ErrorCode.REQUIRED_FIELD_MISSING);
             }
-            else
+
+            var comp = Split(fields[11], compSep);
+            if (comp.Length < 1)
             {
                 throw new HL7Exception(
-                    "Can't find version ID - MSH has only " + fields.Length + " fields.",
+                    $"Can't find version ID - MSH.12 is {fields[11]}",
                     ErrorCode.REQUIRED_FIELD_MISSING);
             }
 
-            return version;
+            return comp[0];
         }
 
         /// <inheritdoc />
@@ -724,10 +723,10 @@ private static EncodingCharacters GetEncodingChars(string message)
         {
             if (message.Length < 9)
             {
-                throw new HL7Exception($"Invalid message content: \"{message}\"");
+                throw new HL7Exception($"Invalid message content: '{message}'");
             }
 
-            return new EncodingCharacters(message[3], message.Substring(4,  4));
+            return new EncodingCharacters(message[3], message.Substring(4, 4));
         }
 
         private static string EncodePrimitive(IPrimitive p, EncodingCharacters encodingChars)

src/NHapi.Base/Util/MessageIterator.cs

@@ -208,7 +208,7 @@ public static Index GetIndex(IGroup parent, IStructure child)
             var names = parent.Names;
             for (var i = 0; i < names.Length; i++)
             {
-                if (names[i].StartsWith(child.GetStructureName()))
+                if (names[i].StartsWith(child.GetStructureName(), StringComparison.Ordinal))
                 {
                     try
                     {

src/NHapi.Base/Util/Terser.cs

@@ -551,7 +551,7 @@ private PathSpec ParsePathSpec(string spec)
         {
             var ps = new PathSpec(this);
 
-            if (spec.StartsWith("."))
+            if (spec.StartsWith(".", StringComparison.Ordinal))
             {
                 ps.Find = true;
                 spec = spec.Substring(1);

src/NHapi.SourceGeneration/Generators/DataTypeGenerator.cs

@@ -30,7 +30,6 @@ namespace NHapi.SourceGeneration.Generators
     using System;
     using System.Collections;
     using System.Data.Common;
-    using System.Data.Odbc;
     using System.IO;
     using System.Linq;
     using System.Text;
@@ -205,7 +204,7 @@ public static void Make(FileInfo targetDirectory, string dataType, string versio
                 // trim all CE_x to CE
                 if (dt != null)
                 {
-                    if (dt.StartsWith("CE"))
+                    if (dt.StartsWith("CE", StringComparison.Ordinal))
                     {
                         dt = "CE";
                     }

src/NHapi.SourceGeneration/Generators/SegmentGenerator.cs

@@ -236,7 +236,7 @@ public static string MakeSegment(string name, string version)
                     se.Type = Convert.ToString(rs[10 - 1]);
 
                     // shorten CE_x to CE
-                    if (se.Type.StartsWith("CE"))
+                    if (se.Type.StartsWith("CE", StringComparison.Ordinal))
                     {
                         se.Type = "CE";
                     }