Replace static DICOM test data with minimal dynamic content

src/SmiServices/Common/Messages/AccessionDirectoryMessage.cs

@@ -3,6 +3,7 @@
 using Newtonsoft.Json;
 using System;
 using System.IO;
+using System.IO.Abstractions;
 
 namespace SmiServices.Common.Messages
 {
@@ -19,7 +20,7 @@ public sealed class AccessionDirectoryMessage : MemberwiseEquatable<AccessionDir
 
         public AccessionDirectoryMessage() { }
 
-        public AccessionDirectoryMessage(string root, DirectoryInfo directory)
+        public AccessionDirectoryMessage(string root, IDirectoryInfo directory)
         {
             if (!directory.FullName.StartsWith(root, StringComparison.CurrentCultureIgnoreCase))
                 throw new Exception("Directory '" + directory + "' did not share a common root with the root '" + root + "'");

src/SmiServices/Common/Messages/DicomFileMessage.cs

@@ -3,6 +3,7 @@
 using Newtonsoft.Json;
 using System;
 using System.IO;
+using System.IO.Abstractions;
 using System.Text;
 
 namespace SmiServices.Common.Messages
@@ -49,7 +50,7 @@ public sealed class DicomFileMessage : MemberwiseEquatable<DicomFileMessage>, IF
 
         public DicomFileMessage() { }
 
-        public DicomFileMessage(string root, FileInfo file)
+        public DicomFileMessage(string root, IFileInfo file)
             : this(root, file.FullName) { }
 
         public DicomFileMessage(string root, string file)

src/SmiServices/Microservices/DicomTagReader/DicomTagReader.cs

@@ -4,6 +4,7 @@
 using SmiServices.Microservices.DicomTagReader.Execution;
 using System;
 using System.Collections.Generic;
+using System.IO.Abstractions;
 
 namespace SmiServices.Microservices.DicomTagReader
 {
@@ -21,12 +22,14 @@ public static int Main(IEnumerable<string> args)
 
         private static int OnParse(GlobalOptions globals, DicomTagReaderCliOptions opts)
         {
+            var fileSystem = new FileSystem();
+
             if (opts.File != null)
             {
                 try
                 {
                     var host = new DicomTagReaderHost(globals);
-                    host.AccessionDirectoryMessageConsumer.RunSingleFile(opts.File);
+                    host.AccessionDirectoryMessageConsumer.RunSingleFile(fileSystem.FileInfo.New(opts.File));
                     return 0;
                 }
                 catch (Exception ex)

src/SmiServices/Microservices/DicomTagReader/DicomTagReaderCliOptions.cs

@@ -1,9 +1,10 @@
 using CommandLine;
 using SmiServices.Common.Options;
-using System.IO;
+using System.Diagnostics.CodeAnalysis;
 
 namespace SmiServices.Microservices.DicomTagReader
 {
+    [ExcludeFromCodeCoverage]
     public class DicomTagReaderCliOptions : CliOptions
     {
         /// <summary>
@@ -15,6 +16,6 @@ public class DicomTagReaderCliOptions : CliOptions
             Required = false,
             HelpText = "[Optional] Name of a specific dicom or zip file to process instead of subscribing to rabbit"
         )]
-        public FileInfo? File { get; set; }
+        public string? File { get; set; }
     }
 }

src/SmiServices/Microservices/DicomTagReader/Messaging/DicomTagReaderConsumer.cs

@@ -4,7 +4,7 @@
 using SmiServices.Common.Options;
 using SmiServices.Microservices.DicomTagReader.Execution;
 using System;
-using System.IO;
+using System.IO.Abstractions;
 
 namespace SmiServices.Microservices.DicomTagReader.Messaging
 {
@@ -15,17 +15,19 @@ public class DicomTagReaderConsumer : Consumer<AccessionDirectoryMessage>
     {
         private readonly TagReaderBase _reader;
         private readonly GlobalOptions _opts;
-
+        private readonly IFileSystem _fileSystem;
 
         /// <summary>
         /// Default constructor
         /// </summary>
         /// <param name="reader"></param>
-        /// <param name="dicomTagReaderOptions"></param>>
-        public DicomTagReaderConsumer(TagReaderBase reader, GlobalOptions dicomTagReaderOptions)
+        /// <param name="dicomTagReaderOptions"></param>
+        /// <param name="fileSystem"></param>>
+        public DicomTagReaderConsumer(TagReaderBase reader, GlobalOptions dicomTagReaderOptions, IFileSystem? fileSystem = null)
         {
             _reader = reader;
             _opts = dicomTagReaderOptions;
+            _fileSystem = fileSystem ?? new FileSystem();
         }
 
         /// <summary>
@@ -61,10 +63,10 @@ protected override void ProcessMessageImpl(IMessageHeader header, AccessionDirec
         /// Runs a single file (dicom or zip) through tag reading process
         /// </summary>
         /// <param name="file"></param>
-        public void RunSingleFile(FileInfo file)
+        public void RunSingleFile(IFileInfo file)
         {
             // tell reader only to consider our specific file
-            _reader.IncludeFile = f => new FileInfo(f).FullName.Equals(file.FullName, StringComparison.CurrentCultureIgnoreCase);
+            _reader.IncludeFile = f => _fileSystem.FileInfo.New(f).FullName.Equals(file.FullName, StringComparison.CurrentCultureIgnoreCase);
             _reader.ReadTags(null, new AccessionDirectoryMessage(_opts.FileSystemOptions!.FileSystemRoot!, file.Directory!));
 
             // good practice to clear this afterwards

tests/SmiServices.IntegrationTests/Microservices/DicomRelationalMapper/DicomRelationalMapperTests.cs

@@ -13,6 +13,7 @@
 using SmiServices.UnitTests.Common;
 using System;
 using System.IO;
+using System.IO.Abstractions;
 using System.Linq;
 using System.Threading;
 using Tests.Common;
@@ -47,9 +48,10 @@ public void Test_DodgyTagNames()
             DirectoryInfo d = new(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_DodgyTagNames)));
             d.Create();
 
-            var td = new TestData();
-            var fi = td.Create(new FileInfo(Path.Combine(d.FullName, "MyTestFile.dcm")));
-            var fi2 = td.Create(new FileInfo(Path.Combine(d.FullName, "MyTestFile2.dcm")));
+            var fileSystem = new FileSystem();
+            var fi = fileSystem.FileInfo.New(fileSystem.Path.Combine(d.FullName, "MyTestFile.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(fi);
+            var fi2 = fileSystem.FileInfo.New(fileSystem.Path.Combine(d.FullName, "MyTestFile2.dcm"));
 
             DicomFile dcm;
 
@@ -113,7 +115,9 @@ public void TestLoadingOneImage_SingleFileMessage(int numberOfMessagesToSend, bo
             DirectoryInfo d = new(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestLoadingOneImage_SingleFileMessage)));
             d.Create();
 
-            var fi = new TestData().Create(new FileInfo(Path.Combine(d.FullName, "MyTestFile.dcm")));
+            var fileSystem = new FileSystem();
+            var fi = fileSystem.FileInfo.New(fileSystem.Path.Combine(d.FullName, "MyTestFile.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(fi);
 
             if (mixInATextFile)
             {
@@ -167,7 +171,7 @@ public void TestLoadingOneImage_MileWideTest()
             d.Create();
 
             var r = new Random(5000);
-            FileInfo[] files;
+            IFileInfo[] files;
 
             using (var g = new DicomDataGenerator(r, d.FullName, "CT"))
                 files = g.GenerateImageFiles(1, r).ToArray();

tests/SmiServices.IntegrationTests/Microservices/DicomRelationalMapper/MicroservicesIntegrationTest.cs

@@ -33,6 +33,7 @@
 using System;
 using System.Data;
 using System.IO;
+using System.IO.Abstractions;
 using System.Linq;
 using System.Text.RegularExpressions;
 using System.Threading;
@@ -122,7 +123,9 @@ public void IntegrationTest_HappyPath(DatabaseType databaseType, Type namerType)
             foreach (var f in dir.GetFiles())
                 f.Delete();
 
-            new TestData().Create(new FileInfo(Path.Combine(dir.FullName, "MyTestFile.dcm")));
+            var fileSystem = new FileSystem();
+            var fi = fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "MyTestFile.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(fi);
 
             RunTest(dir, 1);
         }
@@ -159,7 +162,9 @@ public void IntegrationTest_NoFileExtensions(DatabaseType databaseType, Type nam
             foreach (var f in dir.GetFiles())
                 f.Delete();
 
-            new TestData().Create(new FileInfo(Path.Combine(dir.FullName, "Mr.010101"))); //this is legit a dicom file
+            var fileSystem = new FileSystem();
+            var fi = fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "Mr.010101"));
+            DicomFileTestHelpers.WriteSampleDicomFile(fi);
 
             try
             {
@@ -206,7 +211,9 @@ public void IntegrationTest_Rejector(DatabaseType databaseType, Type? rejector)
             foreach (var f in dir.GetFiles())
                 f.Delete();
 
-            new TestData().Create(new FileInfo(Path.Combine(dir.FullName, "Mr.010101"))); //this is legit a dicom file
+            var fileSystem = new FileSystem();
+            var fi = fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "Mr.010101"));
+            DicomFileTestHelpers.WriteSampleDicomFile(fi);
 
             try
             {
@@ -285,33 +292,36 @@ public void IntegrationTest_HappyPath_WithIsolation(DatabaseType databaseType, T
             foreach (var f in dir.GetFiles())
                 f.Delete();
 
-            new TestData().Create(new FileInfo(Path.Combine(dir.FullName, "MyTestFile.dcm")));
+            var fileSystem = new FileSystem();
+            DicomFileTestHelpers.WriteSampleDicomFile(fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "MyTestFile.dcm")));
 
-            var ds1 = new DicomDataset
-            {
-                { DicomTag.StudyInstanceUID, "1.2.3" },
-                { DicomTag.SeriesInstanceUID, "1.2.2" },
-                { DicomTag.SOPInstanceUID, "1.2.3" },
-                { DicomTag.PatientAge, "030Y" },
-                { DicomTag.PatientID, "123" },
-                { DicomTag.SOPClassUID, "1" },
-                { DicomTag.Modality, "MR" }
-            };
-
-            new DicomFile(ds1).Save(Path.Combine(dir.FullName, "abc.dcm"));
-
-            var ds2 = new DicomDataset
-            {
-                { DicomTag.StudyInstanceUID, "1.2.3" },
-                { DicomTag.SeriesInstanceUID, "1.2.4" },
-                { DicomTag.SOPInstanceUID, "1.2.7" },
-                { DicomTag.PatientAge, "040Y" }, //age is replicated but should be unique at study level so gets isolated
-                { DicomTag.PatientID, "123" },
-                { DicomTag.SOPClassUID, "1" },
-                { DicomTag.Modality, "MR" }
-            };
+            DicomFileTestHelpers.WriteSampleDicomFile(
+                fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "abc.dcm")),
+                new DicomDataset
+                {
+                    { DicomTag.StudyInstanceUID, "1.2.3" },
+                    { DicomTag.SeriesInstanceUID, "1.2.2" },
+                    { DicomTag.SOPInstanceUID, "1.2.3" },
+                    { DicomTag.PatientAge, "030Y" },
+                    { DicomTag.PatientID, "123" },
+                    { DicomTag.SOPClassUID, "1" },
+                    { DicomTag.Modality, "MR" }
+                }
+            );
 
-            new DicomFile(ds2).Save(Path.Combine(dir.FullName, "def.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(
+                fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "def.dcm")),
+                new DicomDataset
+                {
+                    { DicomTag.StudyInstanceUID, "1.2.3" },
+                    { DicomTag.SeriesInstanceUID, "1.2.4" },
+                    { DicomTag.SOPInstanceUID, "1.2.7" },
+                    { DicomTag.PatientAge, "040Y" }, //age is replicated but should be unique at study level so gets isolated
+                    { DicomTag.PatientID, "123" },
+                    { DicomTag.SOPClassUID, "1" },
+                    { DicomTag.Modality, "MR" }
+                }
+            );
 
             var checks = new ProcessTaskChecks(_helper.LoadMetadata);
             checks.Check(new AcceptAllCheckNotifier());
@@ -379,13 +389,24 @@ public void IntegrationTest_HappyPath_WithElevation(DatabaseType databaseType, b
             foreach (var f in dir.GetFiles())
                 f.Delete();
 
-            new TestData().Create(new FileInfo(Path.Combine(dir.FullName, "MyTestFile.dcm")));
+            var ds = DicomFileTestHelpers.DefaultDicomDataset();
+            var sequenceDs = new DicomDataset()
+            {
+                {DicomTag.CodeValue, "CodeValue" },
+                {DicomTag.CodingSchemeDesignator, "CodingSchemeDesignator" },
+                {DicomTag.CodeMeaning, "CodeMeaning" },
+            };
+            ds.Add(new DicomSequence(DicomTag.DerivationCodeSequence, sequenceDs));
+
+            var fileSystem = new FileSystem();
+            var fi = fileSystem.FileInfo.New(fileSystem.Path.Combine(dir.FullName, "MyTestFile.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(fi, ds);
 
             RunTest(dir, 1);
 
             var tbl = _helper.ImageTable.GetDataTable();
             Assert.That(tbl.Rows, Has.Count.EqualTo(1));
-            Assert.That(tbl.Rows[0]["d_DerivationCodeMeaning"], Is.EqualTo("Full fidelity image, uncompressed or lossless compressed"));
+            Assert.That(tbl.Rows[0]["d_DerivationCodeMeaning"], Is.EqualTo("CodeMeaning"));
 
             _helper.ImageTable.DropColumn(_helper.ImageTable.DiscoverColumn("d_DerivationCodeMeaning"));
 

tests/SmiServices.IntegrationTests/Microservices/DicomTagReader/DicomTagReaderHostTests.cs

@@ -5,7 +5,8 @@
 using SmiServices.Microservices.DicomTagReader.Execution;
 using SmiServices.UnitTests.Common;
 using System;
-using System.IO;
+using System.IO.Abstractions;
+using System.IO.Abstractions.TestingHelpers;
 using System.IO.Compression;
 using System.Linq;
 using System.Threading;
@@ -79,7 +80,9 @@ public void TestBasicOperation()
         [Test]
         public void TestTagReader_SingleFileMode()
         {
-            var dirRoot = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.WorkDirectory, "TestTagReader_SingleFileMode"));
+            var fileSystem = new FileSystem();
+
+            var dirRoot = fileSystem.DirectoryInfo.New(fileSystem.Path.Combine(TestContext.CurrentContext.WorkDirectory, "TestTagReader_SingleFileMode"));
 
             if (dirRoot.Exists)
                 dirRoot.Delete(true);
@@ -103,11 +106,11 @@ public void TestTagReader_SingleFileMode()
                 Assert.That(_helper.SeriesCount, Is.EqualTo(1));
             });
 
-            var julyZip = Path.Combine(dirRoot.FullName, "july.zip");
+            var julyZip = fileSystem.Path.Combine(dirRoot.FullName, "july.zip");
 
             ZipFile.CreateFromDirectory(julyFolder.FullName, julyZip);
 
-            host.AccessionDirectoryMessageConsumer.RunSingleFile(new FileInfo(julyZip));
+            host.AccessionDirectoryMessageConsumer.RunSingleFile(fileSystem.FileInfo.New(julyZip));
 
             Assert.Multiple(() =>
             {

tests/SmiServices.IntegrationTests/Microservices/DicomTagReader/DicomTagReaderTests.cs

@@ -0,0 +1,25 @@
+using NUnit.Framework;
+using SmiServices.Common.Options;
+
+namespace SmiServices.IntegrationTests.Microservices.DicomTagReader
+{
+    [RequiresRabbit]
+    public class DicomTagReaderTests
+    {
+        [Test]
+        public void Main_RunSingleFile_Exception_ReturnsOne()
+        {
+            // Arrange
+
+            SmiCliInit.InitSmiLogging = false;
+
+            // Act
+
+            var rc = SmiServices.Microservices.DicomTagReader.DicomTagReader.Main(["-f", "some.dcm"]);
+
+            // Assert
+
+            Assert.That(rc, Is.EqualTo(1));
+        }
+    }
+}

tests/SmiServices.IntegrationTests/Microservices/IsIdentifiable/IsIdentifiableHostTests.cs

@@ -6,6 +6,7 @@
 using SmiServices.UnitTests.Common;
 using System;
 using System.IO;
+using System.IO.Abstractions;
 
 namespace SmiServices.UnitTests.Microservices.IsIdentifiable
 {
@@ -49,8 +50,10 @@ public void TestClassifierName_ValidClassifier()
         {
             var options = new GlobalOptionsFactory().Load(nameof(TestClassifierName_ValidClassifier));
 
-            var testDcm = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm")); Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm");
-            new TestData().Create(testDcm);
+            var fileSystem = new FileSystem();
+            fileSystem.Directory.CreateDirectory(fileSystem.Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier)));
+            var testDcm = fileSystem.FileInfo.New(fileSystem.Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(testDcm);
 
             using var tester = new MicroserviceTester(options.RabbitOptions!, options.IsIdentifiableServiceOptions!);
             tester.CreateExchange(options.IsIdentifiableServiceOptions!.IsIdentifiableProducerOptions!.ExchangeName!, null);
@@ -96,10 +99,9 @@ public void TestIsIdentifiable_TesseractStanfordDicomFileClassifier()
             if (!File.Exists(dest))
                 File.Copy(Path.Combine(DataDirectory, "tessdata", "eng.traineddata"), dest);
 
-            var testDcm = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestIsIdentifiable_TesseractStanfordDicomFileClassifier), "f1.dcm"));
-
-            Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm");
-            new TestData().Create(testDcm);
+            var fileSystem = new FileSystem();
+            var testDcm = fileSystem.FileInfo.New(fileSystem.Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestIsIdentifiable_TesseractStanfordDicomFileClassifier), "f1.dcm"));
+            DicomFileTestHelpers.WriteSampleDicomFile(testDcm);
 
             using var tester = new MicroserviceTester(options.RabbitOptions!, options.IsIdentifiableServiceOptions);
             options.IsIdentifiableServiceOptions.ClassifierType = typeof(TesseractStanfordDicomFileClassifier).FullName;