Add new data type: "Fhir" (#378)

* add fhir datatype * update tests * update tests * fix comment * update tests * fix comments * fix comments Co-authored-by: reviewer <[email protected]>
microsoft · Apr 18, 2022 · 7944d36 · 7944d36
1 parent d7291f8
commit 7944d36
Show file tree

Hide file tree

Showing 15 changed files with 121 additions and 13 deletions.
diff --git a/data/Templates/Stu3ToR4/DataType/_CodeableConceptToCode.liquid b/data/Templates/Stu3ToR4/DataType/_CodeableConceptToCode.liquid
@@ -1,2 +1,2 @@
-{% assign coding = msg.coding | first}
+{% assign coding = msg.coding | first -%}
 "{{coding.code}}"
diff --git a/data/Templates/Stu3ToR4/metadata.json b/data/Templates/Stu3ToR4/metadata.json
@@ -1,3 +1,3 @@
 {
-	"type": "json"
+	"type": "fhir"
 }
diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/FunctionalTests.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/FunctionalTests.cs
@@ -346,12 +346,12 @@ public void GivenCcdaDocument_WhenConverting_ExpectedFhirResourceShouldBeReturne
         [MemberData(nameof(GetDataForStu3ToR4))]
         public void GivenStu3FhirData_WhenConverting_ExpectedR4FhirResourceShouldBeReturned(string rootTemplate, string inputFile, string expectedFile)
         {
-            var jsonProcessor = new JsonProcessor();
+            var fhirProcessor = new FhirProcessor();
             var templateDirectory = Path.Join(AppDomain.CurrentDomain.BaseDirectory, Constants.TemplateDirectory, "Stu3ToR4");
 
             var inputContent = File.ReadAllText(inputFile);
             var expectedContent = File.ReadAllText(expectedFile);
-            var actualContent = jsonProcessor.Convert(inputContent, rootTemplate, new TemplateProvider(templateDirectory, DataType.Json));
+            var actualContent = fhirProcessor.Convert(inputContent, rootTemplate, new TemplateProvider(templateDirectory, DataType.Fhir));
 
             var expectedObject = JObject.Parse(expectedContent);
             var actualObject = JObject.Parse(actualContent);

diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.Tool/ConverterLogicHandler.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.Tool/ConverterLogicHandler.cs
@@ -99,19 +99,14 @@ private static IFhirConverter CreateDataProcessor(DataType dataType)
                 DataType.Hl7v2 => new Hl7v2Processor(),
                 DataType.Ccda => new CcdaProcessor(),
                 DataType.Json => new JsonProcessor(),
+                DataType.Fhir => new FhirProcessor(),
                 _ => throw new NotImplementedException($"The conversion from data type {dataType} to FHIR is not supported")
             };
         }
 
         private static ITemplateProvider CreateTemplateProvider(DataType dataType, string templateDirectory)
         {
-            return dataType switch
-            {
-                DataType.Hl7v2 => new TemplateProvider(templateDirectory, DataType.Hl7v2),
-                DataType.Ccda => new TemplateProvider(templateDirectory, DataType.Ccda),
-                DataType.Json => new TemplateProvider(templateDirectory, DataType.Json),
-                _ => throw new NotImplementedException($"The conversion from data type {dataType} to FHIR is not supported")
-            };
+            return new TemplateProvider(templateDirectory, dataType);
         }
 
         private static TraceInfo CreateTraceInfo(DataType dataType, bool isTraceInfo)
@@ -127,6 +122,7 @@ private static List<string> GetInputFiles(DataType dataType, string inputDataFol
                 DataType.Ccda => Directory.EnumerateFiles(inputDataFolder, "*.*", SearchOption.AllDirectories)
                     .Where(x => CcdaExtensions.Contains(Path.GetExtension(x).ToLower())).ToList(),
                 DataType.Json => Directory.EnumerateFiles(inputDataFolder, "*.json", SearchOption.AllDirectories).ToList(),
+                DataType.Fhir => Directory.EnumerateFiles(inputDataFolder, "*.json", SearchOption.AllDirectories).ToList(),
                 _ => new List<string>(),
             };
         }

diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.UnitTests/Processors/ProcessorTests.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.UnitTests/Processors/ProcessorTests.cs
@@ -20,19 +20,22 @@ public class ProcessorTests
         private static readonly string _hl7v2TestData;
         private static readonly string _ccdaTestData;
         private static readonly string _jsonTestData;
+        private static readonly string _fhirStu3TestData;
 
         static ProcessorTests()
         {
             _hl7v2TestData = File.ReadAllText(Path.Join(TestConstants.SampleDataDirectory, "Hl7v2", "LRI_2.0-NG_CBC_Typ_Message.hl7"));
             _ccdaTestData = File.ReadAllText(Path.Join(TestConstants.SampleDataDirectory, "Ccda", "CCD.ccda"));
             _jsonTestData = File.ReadAllText(Path.Join(TestConstants.SampleDataDirectory, "Json", "ExamplePatient.json"));
+            _fhirStu3TestData = File.ReadAllText(Path.Join(TestConstants.SampleDataDirectory, "Stu3", "Patient.json"));
         }
 
         public static IEnumerable<object[]> GetValidInputsWithTemplateDirectory()
         {
             yield return new object[] { new Hl7v2Processor(), new TemplateProvider(TestConstants.Hl7v2TemplateDirectory, DataType.Hl7v2), _hl7v2TestData, "ORU_R01" };
             yield return new object[] { new CcdaProcessor(), new TemplateProvider(TestConstants.CcdaTemplateDirectory, DataType.Ccda), _ccdaTestData, "CCD" };
             yield return new object[] { new JsonProcessor(), new TemplateProvider(TestConstants.JsonTemplateDirectory, DataType.Json), _jsonTestData, "ExamplePatient" };
+            yield return new object[] { new FhirProcessor(), new TemplateProvider(TestConstants.FhirStu3TemplateDirectory, DataType.Fhir), _fhirStu3TestData, "Patient" };
         }
 
         public static IEnumerable<object[]> GetValidInputsWithTemplateCollection()
@@ -48,6 +51,7 @@ public static IEnumerable<object[]> GetValidInputsWithTemplateCollection()
             yield return new object[] { new Hl7v2Processor(), new TemplateProvider(templateCollection), _hl7v2TestData };
             yield return new object[] { new CcdaProcessor(), new TemplateProvider(templateCollection), _ccdaTestData };
             yield return new object[] { new JsonProcessor(), new TemplateProvider(templateCollection), _jsonTestData };
+            yield return new object[] { new FhirProcessor(), new TemplateProvider(templateCollection), _fhirStu3TestData };
         }
 
         public static IEnumerable<object[]> GetValidInputsWithProcessSettings()
@@ -77,6 +81,11 @@ public static IEnumerable<object[]> GetValidInputsWithProcessSettings()
                 new JsonProcessor(null), new JsonProcessor(new ProcessorSettings()), new JsonProcessor(positiveTimeOutSettings), new JsonProcessor(negativeTimeOutSettings),
                 new TemplateProvider(TestConstants.TestTemplateDirectory, DataType.Json), _jsonTestData,
             };
+            yield return new object[]
+            {
+                new FhirProcessor(null), new FhirProcessor(new ProcessorSettings()), new FhirProcessor(positiveTimeOutSettings), new FhirProcessor(negativeTimeOutSettings),
+                new TemplateProvider(TestConstants.TestTemplateDirectory, DataType.Fhir), _fhirStu3TestData,
+            };
         }
 
         public static IEnumerable<object[]> GetValidInputsWithLargeForLoop()
@@ -99,6 +108,12 @@ public static IEnumerable<object[]> GetValidInputsWithLargeForLoop()
                 new TemplateProvider(TestConstants.TestTemplateDirectory, DataType.Json),
                 _jsonTestData,
             };
+            yield return new object[]
+            {
+                new FhirProcessor(),
+                new TemplateProvider(TestConstants.TestTemplateDirectory, DataType.Fhir),
+                _fhirStu3TestData,
+            };
         }
 
         public static IEnumerable<object[]> GetValidInputsWithNestingTooDeep()
@@ -121,6 +136,12 @@ public static IEnumerable<object[]> GetValidInputsWithNestingTooDeep()
                 new TemplateProvider(TestConstants.TestTemplateDirectory, DataType.Json),
                 _jsonTestData,
             };
+            yield return new object[]
+            {
+                new FhirProcessor(),
+                new TemplateProvider(TestConstants.TestTemplateDirectory, DataType.Fhir),
+                _fhirStu3TestData,
+            };
         }
 
         [Theory]

diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.UnitTests/TestConstants.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.UnitTests/TestConstants.cs
@@ -14,6 +14,7 @@ public static class TestConstants
         public static readonly string Hl7v2TemplateDirectory = Path.Join(TemplateDirectory, "Hl7v2");
         public static readonly string CcdaTemplateDirectory = Path.Join(TemplateDirectory, "Ccda");
         public static readonly string JsonTemplateDirectory = Path.Join(TemplateDirectory, "Json");
+        public static readonly string FhirStu3TemplateDirectory = Path.Join(TemplateDirectory, "Stu3ToR4");
         public static readonly string TestTemplateDirectory = "TestData/TestTemplates";
         public static readonly string ExpectedDirectory = "TestData/Expected/";
     }

diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter/Models/DataType.cs b/src/Microsoft.Health.Fhir.Liquid.Converter/Models/DataType.cs
@@ -13,5 +13,6 @@ public enum DataType
         Hl7v2,
         Ccda,
         Json,
+        Fhir,
     }
 }
diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter/Processors/FhirProcessor.cs b/src/Microsoft.Health.Fhir.Liquid.Converter/Processors/FhirProcessor.cs
@@ -0,0 +1,27 @@
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+
+using Microsoft.Health.Fhir.Liquid.Converter.Models;
+
+namespace Microsoft.Health.Fhir.Liquid.Converter.Processors
+{
+    public class FhirProcessor : JsonProcessor
+    {
+        public FhirProcessor(ProcessorSettings processorSettings = null)
+            : base(processorSettings)
+        {
+        }
+
+        public override string Convert(string data, string rootTemplate, ITemplateProvider templateProvider, TraceInfo traceInfo = null)
+        {
+            // TO DO For FHIR Specific Logic
+            // 1. Add FHIR related checks for pre-processor and post-processor.
+            // 2. Add log for version conversion.
+            // 3. Add logic to process "extension" and "contained" fields.
+
+            return base.Convert(data, rootTemplate, templateProvider, traceInfo);
+        }
+    }
+}
diff --git a/...osoft.Health.Fhir.TemplateManagement.FunctionalTests/TemplateCollectionFunctionalTests.cs b/...osoft.Health.Fhir.TemplateManagement.FunctionalTests/TemplateCollectionFunctionalTests.cs
@@ -37,6 +37,7 @@ public class TemplateCollectionFunctionalTests : IAsyncLifetime
         private readonly string _defaultHl7v2TemplateImageReference = "microsofthealth/hl7v2templates:default";
         private readonly string _defaultCcdaTemplateImageReference = "microsofthealth/ccdatemplates:default";
         private readonly string _defaultJsonTemplateImageReference = "microsofthealth/jsontemplates:default";
+        private readonly string _defaultStu3ToR4TemplateImageReference = "microsofthealth/stu3tor4templates:default";
         private readonly string testOneLayerImageReference;
         private readonly string testMultiLayerImageReference;
         private readonly string testInvalidImageReference;
@@ -150,6 +151,28 @@ public static IEnumerable<object[]> GetJsonDataAndTemplateSources()
             });
         }
 
+        public static IEnumerable<object[]> GetFhirStu3DataAndTemplateSources()
+        {
+            var data = new List<string>
+            {
+                @"CapabilityStatement",
+                @"CodeSystem",
+                @"Observation",
+                @"OperationDefinition",
+                @"OperationOutcome",
+                @"Parameters",
+                @"Patient",
+                @"StructureDefinition",
+                @"ValueSet",
+            };
+            return data.Select(item => new[]
+            {
+                Path.Join(_sampleDataDirectory, "Stu3", $"{item}.json"),
+                Path.Join(_templateDirectory, "Stu3ToR4"),
+                item,
+            });
+        }
+
         public static IEnumerable<object[]> GetNotExistImageInfo()
         {
             yield return new object[] { "templatetest", "notexist" };
@@ -173,6 +196,7 @@ public static IEnumerable<object[]> GetDefaultTemplatesInfo()
             yield return new object[] { "microsofthealth/hl7v2templates:default", "Hl7v2" };
             yield return new object[] { "microsofthealth/ccdatemplates:default", "Ccda" };
             yield return new object[] { "microsofthealth/jsontemplates:default", "Json" };
+            yield return new object[] { "microsofthealth/stu3tor4templates:default", "Stu3ToR4" };
         }
 
         [Fact]
@@ -399,6 +423,28 @@ public async Task GivenJsonSameInputData_WithDifferentTemplateSource_WhenConvert
             Assert.True(JToken.DeepEquals(imageResultObject, folderResultObject));
         }
 
+        [Theory]
+        [MemberData(nameof(GetFhirStu3DataAndTemplateSources))]
+        public async Task GivenFhirStu3SameInputData_WithDifferentTemplateSource_WhenConvert_ResultShouldBeIdentical(string inputFile, string defaultTemplateDirectory, string rootTemplate)
+        {
+            var folderTemplateProvider = new TemplateProvider(defaultTemplateDirectory, DataType.Fhir);
+
+            var templateProviderFactory = new TemplateCollectionProviderFactory(new MemoryCache(new MemoryCacheOptions()), Options.Create(new TemplateCollectionConfiguration()));
+            var templateProvider = templateProviderFactory.CreateTemplateCollectionProvider(_defaultStu3ToR4TemplateImageReference, string.Empty);
+            var imageTemplateProvider = new TemplateProvider(await templateProvider.GetTemplateCollectionAsync(CancellationToken.None));
+
+            var fhirProcessor = new FhirProcessor();
+            var inputContent = File.ReadAllText(inputFile);
+
+            var imageResult = fhirProcessor.Convert(inputContent, rootTemplate, imageTemplateProvider);
+            var folderResult = fhirProcessor.Convert(inputContent, rootTemplate, folderTemplateProvider);
+
+            var imageResultObject = JObject.Parse(imageResult);
+            var folderResultObject = JObject.Parse(folderResult);
+
+            Assert.True(JToken.DeepEquals(imageResultObject, folderResultObject));
+        }
+
         private void TestByTemplate(string inputFile, string entryTemplate, List<Dictionary<string, Template>> templateProvider)
         {
             var hl7v2Processor = new Hl7v2Processor();

diff --git a/src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/Models/DefaultTemplateInfoTest.cs b/src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/Models/DefaultTemplateInfoTest.cs
@@ -19,6 +19,7 @@ public static IEnumerable<object[]> GetValidDefaultTemplateInfo()
             yield return new object[] { DataType.Hl7v2, "microsofthealth/hl7v2templates:default", "Hl7v2DefaultTemplates.tar.gz" };
             yield return new object[] { DataType.Ccda, "microsofthealth/ccdatemplates:default", "CcdaDefaultTemplates.tar.gz" };
             yield return new object[] { DataType.Json, "microsofthealth/jsontemplates:default", "JsonDefaultTemplates.tar.gz" };
+            yield return new object[] { DataType.Fhir, "microsofthealth/stu3tor4templates:default", "Stu3ToR4DefaultTemplates.tar.gz" };
         }
 
         public static IEnumerable<object[]> GetSupportedImageReference()
@@ -27,6 +28,7 @@ public static IEnumerable<object[]> GetSupportedImageReference()
             yield return new object[] { "microsofthealth/hl7v2templates:default" };
             yield return new object[] { "microsofthealth/ccdatemplates:default" };
             yield return new object[] { "microsofthealth/jsontemplates:default" };
+            yield return new object[] { "microsofthealth/stu3tor4templates:default" };
         }
 
         public static IEnumerable<object[]> GetSupportedImageReferenceWithCaseInsensitive()
@@ -37,6 +39,7 @@ public static IEnumerable<object[]> GetSupportedImageReferenceWithCaseInsensitiv
             yield return new object[] { "MICROSOFTHEALTH/hl7v2templates:default" };
             yield return new object[] { "microsofthealth/ccdatemplates:DEFAULT" };
             yield return new object[] { "microsofthealth/JSONtemplates:DEFAULT" };
+            yield return new object[] { "microsofthealth/STU3ToR4templates:DEFAULT" };
         }
 
         public static IEnumerable<object[]> GetUnSupportedImageReference()

diff --git a/src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/Models/ImageInfoTest.cs b/src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/Models/ImageInfoTest.cs
@@ -84,6 +84,7 @@ public static IEnumerable<object[]> GetDefaultTemplateReference()
             yield return new object[] { "microsofthealth/hl7v2templates:default" };
             yield return new object[] { "microsofthealth/ccdatemplates:default" };
             yield return new object[] { "microsofthealth/jsontemplates:default" };
+            yield return new object[] { "microsofthealth/stu3tor4templates:default" };
         }
 
         public static IEnumerable<object[]> GetDefaultTemplateReferenceWithCaseInsensitive()
@@ -95,6 +96,7 @@ public static IEnumerable<object[]> GetDefaultTemplateReferenceWithCaseInsensiti
             yield return new object[] { "MicrosoftHealth/Hl7v2Templates:default" };
             yield return new object[] { "microsoftHealth/CcdaTemplates:default" };
             yield return new object[] { "microsoftHealth/JSONTemplates:default" };
+            yield return new object[] { "microsoftHealth/STu3tor4Templates:default" };
         }
 
         public static IEnumerable<object[]> GetInvalidDefaultTemplateReference()

diff --git a/...oft.Health.Fhir.TemplateManagement.UnitTests/Providers/TemplateCollectionProviderTests.cs b/...oft.Health.Fhir.TemplateManagement.UnitTests/Providers/TemplateCollectionProviderTests.cs
@@ -41,6 +41,8 @@ public TemplateCollectionProviderTests()
             _cache.Set("microsofthealth/ccdatemplates:default", ccdaDefaultTemplateLayer, memoryOption);
             TemplateLayer jsonDefaultTemplateLayer = TemplateLayer.ReadFromEmbeddedResource("JsonDefaultTemplates.tar.gz");
             _cache.Set("microsofthealth/jsontemplates:default", jsonDefaultTemplateLayer, memoryOption);
+            TemplateLayer stu3ToR4DefaultTemplateLayer = TemplateLayer.ReadFromEmbeddedResource("Stu3ToR4DefaultTemplates.tar.gz");
+            _cache.Set("microsofthealth/stu3tor4templates:default", stu3ToR4DefaultTemplateLayer, memoryOption);
 
             PushLargeSizeManifest();
         }
@@ -85,10 +87,11 @@ public static IEnumerable<object[]> GetImageInfoForArtifactWithTag()
 
         public static IEnumerable<object[]> GetDefaultTemplatesInfo()
         {
-            yield return new object[] { "microsofthealth/fhirconverter:default", 852 };
-            yield return new object[] { "microsofthealth/hl7v2templates:default", 852 };
+            yield return new object[] { "microsofthealth/fhirconverter:default", 915 };
+            yield return new object[] { "microsofthealth/hl7v2templates:default", 915 };
             yield return new object[] { "microsofthealth/ccdatemplates:default", 821 };
             yield return new object[] { "microsofthealth/jsontemplates:default", 2 };
+            yield return new object[] { "microsofthealth/stu3tor4templates:default", 261 };
         }
 
         [Theory]

diff --git a/...rosoft.Health.Fhir.TemplateManagement.UnitTests/TemplateCollectionProviderFactoryTests.cs b/...rosoft.Health.Fhir.TemplateManagement.UnitTests/TemplateCollectionProviderFactoryTests.cs
@@ -26,6 +26,7 @@ public class TemplateCollectionProviderFactoryTests
         private static readonly string _defaultHl7v2TemplateImageReference = "microsofthealth/hl7v2templates:default";
         private static readonly string _defaultCcdaTemplateImageReference = "microsofthealth/ccdatemplates:default";
         private static readonly string _defaultJsonTemplateImageReference = "microsofthealth/jsontemplates:default";
+        private static readonly string _defaultStu3ToR4TemplateImageReference = "microsofthealth/stu3tor4templates:default";
 
         public static IEnumerable<object[]> GetValidImageInfoWithTag()
         {
@@ -45,6 +46,7 @@ public static IEnumerable<object[]> GetDefaultTemplateTarGzFile()
             yield return new object[] { "Hl7v2NewDefaultTemplates.tar.gz", _defaultHl7v2TemplateImageReference, Path.Join(_testTemplatesPath, "Hl7v2") };
             yield return new object[] { "CcdaNewDefaultTemplates.tar.gz", _defaultCcdaTemplateImageReference, Path.Join(_testTemplatesPath, "Ccda") };
             yield return new object[] { "JsonNewDefaultTemplates.tar.gz", _defaultJsonTemplateImageReference, Path.Join(_testTemplatesPath, "Json") };
+            yield return new object[] { "Stu3ToR4NewDefaultTemplates.tar.gz", _defaultStu3ToR4TemplateImageReference, Path.Join(_testTemplatesPath, "Stu3ToR4") };
         }
 
         public static IEnumerable<object[]> GetDefaultImageReference()
@@ -53,6 +55,7 @@ public static IEnumerable<object[]> GetDefaultImageReference()
             yield return new object[] { _defaultHl7v2TemplateImageReference };
             yield return new object[] { _defaultCcdaTemplateImageReference };
             yield return new object[] { _defaultJsonTemplateImageReference };
+            yield return new object[] { _defaultStu3ToR4TemplateImageReference };
         }
 
         [Theory]
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,5 +13,6 @@ public enum DataType @@
             Hl7v2,
             Ccda,
             Json,
+            Fhir,
         }
     }