Transfer project

.github/workflows/dotnet.yml

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+name: .NET
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v1
+      with:
+        dotnet-version: 5.0.x
+    - name: Restore dependencies
+      run: dotnet restore
+    - name: Build
+      run: dotnet build --no-restore
+    - name: Test
+      run: dotnet test --no-build --verbosity normal

Healex.HL7v2Anonymizer.Tests/AnonymizerTests.cs

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+using HL7.Dotnetcore;
+using Microsoft.Extensions.Configuration;
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+using System;
+using System.IO;
+using static Healex.HL7v2Anonymizer.ReplacementOptions;
+
+namespace Healex.HL7v2Anonymizer.Tests
+{
+    [TestClass]
+    public class AnonymizerTests
+    {
+        [TestMethod]
+        [DeploymentItem("Healex.HL7v2Anonymizer.Tests/TestData", "TestData")]
+        public void AnonymizerTestAdt()
+        {
+            TestAnonymization(File.ReadAllText(@"./TestData/TestAdt1.hl7"));
+        }
+
+        [TestMethod]
+        [DeploymentItem("Healex.HL7v2Anonymizer.Tests/TestData", "TestData")]
+        public void AnonymizerTestOru()
+        {
+            TestAnonymization(File.ReadAllText(@"./TestData/TestOru1.hl7"));
+        }
+
+        public void TestAnonymization(string messageContent)
+        {
+            var message = new Message(messageContent);
+
+            // Setup
+            var replacementOptions = getReplacementOptions();
+            message.ParseMessage();
+
+            // Method under test
+            var anonymizer = new Anonymizer(replacementOptions);
+            anonymizer.Anonymize(message);
+
+            // Assert
+            foreach (SegmentReplacement segment in replacementOptions.Segments)
+            {
+                foreach (Replacement replacement in segment.Replacements)
+                {
+                    try
+                    {
+                        Assert.AreEqual(message.GetValue(replacement.Path), replacement.Value);
+                    }
+                    catch (HL7Exception)
+                    {
+                        // Throws if segment is not present
+                        continue;
+                    }
+                }
+            }
+
+            // Output for manual inspection
+            var messageAsString = message.SerializeMessage(true);
+            Console.WriteLine(messageAsString);
+        }
+
+        private static ReplacementOptions getReplacementOptions()
+        {
+            var builder = new ConfigurationBuilder()
+                .SetBasePath(Directory.GetCurrentDirectory())
+                .AddJsonFile("appsettings.json", optional: false);
+
+            IConfiguration config = builder.Build();
+
+            var replacementOptions = config.GetSection("ReplacementOptions").Get<ReplacementOptions>();
+            return replacementOptions;
+        }
+    }
+}

Healex.HL7v2Anonymizer.Tests/Healex.HL7v2Anonymizer.Tests.csproj

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+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net5.0</TargetFramework>
+
+    <IsPackable>false</IsPackable>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <Content Include="..\Healex.HL7v2Anonymizer\appsettings.json" Link="appsettings.json" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Microsoft.Extensions.Configuration" Version="5.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Hosting.Abstractions" Version="5.0.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.7.1" />
+    <PackageReference Include="MSTest.TestAdapter" Version="2.1.1" />
+    <PackageReference Include="MSTest.TestFramework" Version="2.1.1" />
+    <PackageReference Include="coverlet.collector" Version="1.3.0" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Healex.HL7v2Anonymizer\Healex.HL7v2Anonymizer.csproj" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <None Update="TestData\TestAdt1.hl7">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="TestData\TestOru1.hl7">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+  </ItemGroup>
+
+</Project>

Healex.HL7v2Anonymizer.Tests/TestData/TestAdt1.hl7

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+MSH|^~\&|NES|NINTENDO|TESTSYSTEM|TESTFACILITY|20010101000000||ADT^A04|Q123456789T123456789X123456|P|2.3
+EVN|A04|20010101000000|||^KOOPA^BOWSER^^^^^^^CURRENT
+PID|1||123456789^^^^MR||BROS^MARIO^^^^||19850101000000|M|||123 FAKE STREET^MARIO LUIGI BROS PLACE^TOADSTOOL KINGDOM^NES^A1B2C3^JP^HOME^^1234|1234|(555)555-0123^HOME^JP:1234567^^1^555^5550123~(555)555-0124^HOME^JP:1234568^^1^555^5550124|||S|MSH|12345678|||||||0|||||N
+NK1|1|PEACH^PRINCESS^^^^|SO|ANOTHER CASTLE^^TOADSTOOL KINGDOM^NES^^JP|(123)555-1234|(123)555-2345|NOK|||||||||||||
+NK1|2|TOADSTOOL^PRINCESS^^^^|SO|YET ANOTHER CASTLE^^TOADSTOOL KINGDOM^NES^^JP|(123)555-3456|(123)555-4567|EMC|||||||||||||
+PV1|1|O|ABCD^EFGH^|||^^|123456^DINO^YOSHI^^^^^^MSRM^CURRENT^^^NEIGHBOURHOOD DR NBR^|^DOG^DUCKHUNT^^^^^^^CURRENT||CRD|||||||123456^DINO^YOSHI^^^^^^MSRM^CURRENT^^^NEIGHBOURHOOD DR NBR^|AO|0123456789|1|||||||||||||||||||MSH||A|||20010101000000
+IN1|1|PAR^PARENT||||LUIGI
+IN1|2|FRI^FRIEND||||PRINCESS

Healex.HL7v2Anonymizer.Tests/TestData/TestOru1.hl7

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+MSH|^~\&|LCS|LCA|LIS|TEST9999|199807311532||ORU^R01|3629|P|2.2
+PID|2|2161348462|20809880170|1614614|20809880170^TESTPAT||19760924|M|||^^^^
+ORC|NW|8642753100012^LIS|20809880170^LCS||||||19980727000000|||HAVILAND
+OBR|1|8642753100012^LIS|20809880170^LCS|008342^UPPER RESPIRATORY
+OBX|1|ST|008342^UPPER RESPIRATORY CULTURE^L||FINALREPORT|||||N|F||| 19980729160500|BN
+ORC|NW|8642753100012^LIS|20809880170^LCS||||||19980727000000|||HAVILAND
+OBR|2|8642753100012^LIS|20809880170^LCS|997602^.^L|||19980727175800||||G|||
+OBX|2|CE|997231^RESULT 1^L||M415|||||N|F|||19980729160500|BN
+NTE|1|L|MORAXELLA (BRANHAMELLA) CATARRHALIS
+NTE|2|L| HEAVY GROWTH
+NTE|3|L| BETA LACTAMASE POSITIVE
+OBX|3|CE|997232^RESULT 2^L||MR105|||||N|F|||19980729160500|BN
+NTE|1|L|ROUTINE RESPIRATORY FLORA

Healex.HL7v2Anonymizer.sln

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+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 16
+VisualStudioVersion = 16.0.31005.135
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Healex.HL7v2Anonymizer", "Healex.HL7v2Anonymizer\Healex.HL7v2Anonymizer.csproj", "{9A79221A-7684-4BD6-9721-199934853893}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Healex.HL7v2Anonymizer.Tests", "Healex.HL7v2Anonymizer.Tests\Healex.HL7v2Anonymizer.Tests.csproj", "{2B44D800-3F01-4288-AFD1-1DF7D956B661}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{9A79221A-7684-4BD6-9721-199934853893}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{9A79221A-7684-4BD6-9721-199934853893}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{9A79221A-7684-4BD6-9721-199934853893}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{9A79221A-7684-4BD6-9721-199934853893}.Release|Any CPU.Build.0 = Release|Any CPU
+		{2B44D800-3F01-4288-AFD1-1DF7D956B661}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{2B44D800-3F01-4288-AFD1-1DF7D956B661}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{2B44D800-3F01-4288-AFD1-1DF7D956B661}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{2B44D800-3F01-4288-AFD1-1DF7D956B661}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {971ACC78-6922-482C-8AC1-693787A35B0B}
+	EndGlobalSection
+EndGlobal

Healex.HL7v2Anonymizer/Anonymizer.cs

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+using HL7.Dotnetcore;
+using System;
+using static Healex.HL7v2Anonymizer.ReplacementOptions;
+
+namespace Healex.HL7v2Anonymizer
+{
+    public class Anonymizer
+    {
+        private ReplacementOptions _replacementOptions;
+
+        public Anonymizer(ReplacementOptions replacementOptions)
+        {
+            _replacementOptions = replacementOptions;
+        }
+
+        public bool Anonymize(Message message)
+        {
+            var isSuccess = true;
+            foreach (SegmentReplacement segmentReplacement in _replacementOptions.Segments)
+            {
+                var segments = message.Segments(segmentReplacement.Segment);
+                foreach (Segment segment in segments)
+                {
+                    // Create new temporary message for each repeating segment 
+                    // because we can't set values in all repeating segments at once
+                    // We use references so this overwrites the original segments
+                    var tempMessage = new Message();
+                    tempMessage.AddNewSegment(segment);
+
+                    foreach (Replacement replacement in segmentReplacement.Replacements)
+                    {
+                        tryReplaceValue(replacement, tempMessage);
+                    }
+                }
+            }
+            return isSuccess;
+        }
+
+        private bool tryReplaceValue(Replacement replacement, Message message)
+        {
+            try
+            {
+                message.SetValue(replacement.Path, replacement.Value);
+            }
+            catch (HL7Exception)
+            {
+                // Throws if segment is not present
+            }
+            catch (Exception e)
+            {
+                Console.WriteLine(e.Message);
+                return false;
+            }
+            return true;
+        }
+    }
+
+
+}

Healex.HL7v2Anonymizer/Healex.HL7v2Anonymizer.csproj

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+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>net5.0</TargetFramework>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="HL7-dotnetcore" Version="2.20.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration" Version="5.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Hosting" Version="5.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Hosting.Abstractions" Version="5.0.0" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <None Update="appsettings.json">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+  </ItemGroup>
+
+</Project>

Healex.HL7v2Anonymizer/Program.cs

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+using HL7.Dotnetcore;
+using Microsoft.Extensions.Configuration;
+using System;
+using System.IO;
+
+namespace Healex.HL7v2Anonymizer
+{
+    class Program
+    {
+        static void Main(string[] args)
+        {
+            waitForInput();
+        }
+
+        private static void waitForInput()
+        {
+            Console.WriteLine("Welcome to the Healex HL7v2 anonymizer!");
+            Console.WriteLine("---------------------------------------------------------------------------------------");
+            Console.WriteLine("WARNING: THIS APPLICATION OVERWRITES THE ORIGINAL v2 MESSAGES. BACKUP YOUR FILES FIRST!");
+            Console.WriteLine("---------------------------------------------------------------------------------------");
+            Console.WriteLine("Enter the directory to your v2 messages and press enter:");
+            var directory = Console.ReadLine();
+            Console.WriteLine();
+            tryAnonymizeMessages(directory);
+            Console.WriteLine();
+            waitForInput();
+        }
+
+        private static void tryAnonymizeMessages(string directory)
+        {
+            var pathsToV2Messages = getPathsToV2Messages(directory);
+            var anonymizer = new Anonymizer(getReplacementOptions());
+
+            if (pathsToV2Messages is not null)
+            {
+                if (pathsToV2Messages.Length == 0)
+                    Console.WriteLine($"=> No v2 messages found in {directory}");
+
+                foreach (string path in pathsToV2Messages)
+                {
+                    var message = readAndParseMessage(path);
+                    var success = anonymizer.Anonymize(message);
+                    serializeAndWriteMessageOrLogError(success, message, path);
+                }
+            }
+        }
+
+        private static void serializeAndWriteMessageOrLogError(bool success, Message message, string path)
+        {
+            if (success)
+            {
+                Console.WriteLine($"=> Anonymization successful: {path}");
+                var serializedMessage = message.SerializeMessage(true);
+                File.WriteAllText(path, serializedMessage);
+            }
+            else
+            {
+                Console.WriteLine($"=> Anonymization fail: {path}");
+            }
+        }
+
+        private static string[] getPathsToV2Messages(string directory)
+        {
+            try
+            {
+                var v2Messages = Directory.GetFiles(directory, "*.hl7");
+                return v2Messages;
+            }
+            catch (Exception e)
+            {
+                Console.WriteLine(e.Message);
+                return null;
+            }
+        }
+
+        private static Message readAndParseMessage(string path)
+        {
+            try
+            {
+                var message = new Message(File.ReadAllText(path));
+                message.ParseMessage();
+                return message;
+            } catch (Exception e)
+            {
+                Console.Write(e.Message);
+                return null;
+            }
+        }
+
+        private static ReplacementOptions getReplacementOptions()
+        {
+            var builder = new ConfigurationBuilder()
+                .SetBasePath(Directory.GetCurrentDirectory())
+                .AddJsonFile("appsettings.json", optional: false);
+
+            IConfiguration config = builder.Build();
+
+            var replacementOptions = config.GetSection("ReplacementOptions").Get<ReplacementOptions>();
+            return replacementOptions;
+        }
+    }
+}

Healex.HL7v2Anonymizer/ReplacementOptions.cs

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+namespace Healex.HL7v2Anonymizer
+{
+    public class ReplacementOptions
+    {
+        public SegmentReplacement[] Segments { get; set; }
+
+        public class SegmentReplacement
+        {
+            public string Segment { get; set; }
+            public Replacement[] Replacements { get; set; }
+        }
+
+        public class Replacement
+        {
+            public string Path { get; set; }
+            public string Value { get; set; }
+        }
+    }
+}