Added String Value Type for FHIR Mapping transformation (#46)

* Add string value type for CodeValueFhir templates * Updated documentation for new string value type. * Fix unit test to reflect real and valid FHIR component format Co-authored-by: Maurizio Macagno <[email protected]>
microsoft · May 27, 2020 · 9f7cf74 · 9f7cf74
1 parent 173145c
commit 9f7cf74
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diff --git a/docs/Configuration.md b/docs/Configuration.md
@@ -333,7 +333,14 @@ The CodeValueFhirTemplate is currently the only template supported in FHIR mappi
 |**Components[].Value**|The value to extract and represent in the component. See [Value Type Templates](#valuetypes) for more information.
 
 ## Value Type Templates <a name="valuetypes"></a>
+Each Value type defines at least the following properties:
+| Property | Description 
+| --- | ---
+|**ValueType**|The type of this value. One of the value type templates below. 
+|**ValueName**|The name of the attribute projected by the normalization phase. 
+
 Below are the currently supported value type templates. In the future further templates may be added.
+
 ### SampledData
 Represents the [SampledData](http://hl7.org/fhir/datatypes.html#SampledData) FHIR data type. Measurements are written to value stream starting with start of the observations and incrementing forward using the period defined.  If no value is present an `E` will be written into the data stream.  If the period is such that two more values occupy the same position in the data stream the latest value is used.  The same logic is applied when an observation using the SampledData is updated.
 
@@ -351,6 +358,11 @@ Represents the [Quantity](http://hl7.org/fhir/datatypes.html#Quantity) FHIR data
 |**Code**| Coded form of the unit.
 |**System**| System that defines the coded unit form.
 
+### String
+Represent the [string](https://www.hl7.org/fhir/datatypes.html#string) FHIR data type. If more than one value is present in the grouping only the first value is used. If new value arrives that maps to the same observation it will overwrite the old value.
+
+No additional properties are defined.
+
 ### CodeableConcept
 Represents the [CodeableConcept](http://hl7.org/fhir/datatypes.html#CodeableConcept) FHIR data type. The actual value isn't used.
 

diff --git a/src/lib/Microsoft.Health.Fhir.Ingest/Template/StringFhirValueType.cs b/src/lib/Microsoft.Health.Fhir.Ingest/Template/StringFhirValueType.cs
@@ -0,0 +1,11 @@
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+
+namespace Microsoft.Health.Fhir.Ingest.Template
+{
+    public class StringFhirValueType : FhirValueType
+    {
+    }
+}
diff --git a/src/lib/Microsoft.Health.Fhir.R4.Ingest/Template/R4FhirValueProcessor.cs b/src/lib/Microsoft.Health.Fhir.R4.Ingest/Template/R4FhirValueProcessor.cs
@@ -15,7 +15,8 @@ public R4FhirValueProcessor()
             : base(
                 new SampledDataFhirValueProcessor(),
                 new CodeableConceptFhirValueProcessor(),
-                new QuantityFhirValueProcessor())
+                new QuantityFhirValueProcessor(),
+                new StringFhirValueProcessor())
         {
         }
     }

diff --git a/src/lib/Microsoft.Health.Fhir.R4.Ingest/Template/StringFhirValueProcessor.cs b/src/lib/Microsoft.Health.Fhir.R4.Ingest/Template/StringFhirValueProcessor.cs
@@ -0,0 +1,34 @@
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using EnsureThat;
+using Hl7.Fhir.Model;
+
+namespace Microsoft.Health.Fhir.Ingest.Template
+{
+    public class StringFhirValueProcessor : FhirValueProcessor<StringFhirValueType, (DateTime start, DateTime end, IEnumerable<(DateTime, string)> values), Element>
+    {
+        protected override Element CreateValueImpl(StringFhirValueType template, (DateTime start, DateTime end, IEnumerable<(DateTime, string)> values) inValue)
+        {
+            EnsureArg.IsNotNull(template, nameof(template));
+
+            return new FhirString(inValue.values.Single().Item2);
+        }
+
+        protected override Element MergeValueImpl(StringFhirValueType template, (DateTime start, DateTime end, IEnumerable<(DateTime, string)> values) inValue, Element existingValue)
+        {
+            if (!(existingValue is FhirString))
+            {
+                throw new NotSupportedException($"Element {nameof(existingValue)} expected to be of type {typeof(FhirString)}.");
+            }
+
+            // Only a single value, just replace.
+            return CreateValueImpl(template, inValue);
+        }
+    }
+}
diff --git a/test/Microsoft.Health.Fhir.Ingest.UnitTests/Microsoft.Health.Fhir.Ingest.UnitTests.csproj b/test/Microsoft.Health.Fhir.Ingest.UnitTests/Microsoft.Health.Fhir.Ingest.UnitTests.csproj
@@ -45,6 +45,12 @@
     <None Update="TestInput\data_CodeValueFhirTemplate_CodeableConceptData.json">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="TestInput\data_CodeValueFhirTemplate_CodeableConceptAndStringComponent.json">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="TestInput\data_CodeValueFhirTemplate_String.json">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="TestInput\data_CodeValueFhirTemplate_Quantity.json">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>

diff --git a/test/Microsoft.Health.Fhir.Ingest.UnitTests/Template/CodeValueFhirTemplateFactoryTests.cs b/test/Microsoft.Health.Fhir.Ingest.UnitTests/Template/CodeValueFhirTemplateFactoryTests.cs
@@ -196,6 +196,90 @@ public void GivenValidTemplateJsonWithComponentValueQuantityType_WhenFactoryCrea
                 });
         }
 
+        [Theory]
+        [FileData(@"TestInput/data_CodeValueFhirTemplate_String.json")]
+        public void GivenValidTemplateJsonWithValueStringType_WhenFactoryCreate_ThenTemplateCreated_Test(string json)
+        {
+            var templateContainer = JsonConvert.DeserializeObject<TemplateContainer>(json);
+
+            var factory = new CodeValueFhirTemplateFactory();
+
+            var template = factory.Create(templateContainer);
+            Assert.NotNull(template);
+
+            var codeValueTemplate = template as CodeValueFhirTemplate;
+            Assert.NotNull(codeValueTemplate);
+
+            Assert.Equal("stringDetail", codeValueTemplate.TypeName);
+            Assert.Equal(ObservationPeriodInterval.Single, codeValueTemplate.PeriodInterval);
+            Assert.NotNull(codeValueTemplate.Value);
+
+            var value = codeValueTemplate.Value as StringFhirValueType;
+            Assert.NotNull(value);
+            Assert.Equal("reasonText", value.ValueName);
+
+            Assert.Null(codeValueTemplate.Codes);
+        }
+
+        [Theory]
+        [FileData(@"TestInput/data_CodeValueFhirTemplate_CodeableConceptAndStringComponent.json")]
+        public void GivenValidTemplateJsonWithMixedMainAndComponentValues_WhenFactoryCreate_ThenTemplateCreated_Test(string json)
+        {
+            var templateContainer = JsonConvert.DeserializeObject<TemplateContainer>(json);
+
+            var factory = new CodeValueFhirTemplateFactory();
+
+            var template = factory.Create(templateContainer);
+            Assert.NotNull(template);
+
+            var codeValueTemplate = template as CodeValueFhirTemplate;
+            Assert.NotNull(codeValueTemplate);
+
+            Assert.Equal("alarmEvent", codeValueTemplate.TypeName);
+            Assert.Equal(ObservationPeriodInterval.Single, codeValueTemplate.PeriodInterval);
+            Assert.NotNull(codeValueTemplate.Value);
+
+            var value = codeValueTemplate.Value as CodeableConceptFhirValueType;
+            Assert.NotNull(value);
+            Assert.Equal("alarm", value.ValueName);
+            Assert.Equal("Alarm!", value.Text);
+            Assert.Collection(
+                value.Codes,
+                c =>
+                {
+                    Assert.Equal("alarmEvent", c.Code);
+                    Assert.Equal("https://www.contoso.com/events/v1", c.System);
+                    Assert.Equal("Alarm Event", c.Display);
+                });
+
+            Assert.Collection(
+                codeValueTemplate.Codes,
+                c =>
+                {
+                    Assert.Equal("deviceEvent", c.Code);
+                    Assert.Equal("https://www.contoso.com/events/v1", c.System);
+                    Assert.Equal("Device Event", c.Display);
+                });
+
+            Assert.Collection(
+                codeValueTemplate.Components,
+                c =>
+                {
+                    var stringValue = c.Value as StringFhirValueType;
+                    Assert.NotNull(stringValue);
+                    Assert.Equal("reason", stringValue.ValueName);
+
+                    Assert.Collection(
+                        c.Codes,
+                        cd =>
+                        {
+                            Assert.Equal("reasonText", cd.Code);
+                            Assert.Equal("https://www.contoso.com/events/v1", cd.System);
+                            Assert.Equal("Reason Text", cd.Display);
+                        });
+                });
+        }
+
         [Fact]
         public void GivenInvalidTemplateTargetType_WhenFactoryCreate_ThenInvalidTemplateExceptionThrown_Test()
         {

diff --git a/...est.UnitTests/TestInput/data_CodeValueFhirTemplate_CodeableConceptAndStringComponent.json b/...est.UnitTests/TestInput/data_CodeValueFhirTemplate_CodeableConceptAndStringComponent.json
@@ -0,0 +1,41 @@
+{
+  "templateType": "CodeValueFhir",
+  "template": {
+    "codes": [
+      {
+        "code": "deviceEvent",
+        "system": "https://www.contoso.com/events/v1",
+        "display": "Device Event"
+      }
+    ],
+    "periodInterval": 0,
+    "typeName": "alarmEvent",
+    "value": {
+      "text": "Alarm!",
+      "codes": [
+        {
+          "code": "alarmEvent",
+          "system": "https://www.contoso.com/events/v1",
+          "display": "Alarm Event"
+        }
+      ],
+      "valueName": "alarm",
+      "valueType": "CodeableConcept"
+    },
+    "components": [
+      {
+        "codes": [
+          {
+            "code": "reasonText",
+            "display": "Reason Text",
+            "system": "https://www.contoso.com/events/v1"
+          }
+        ],
+        "value": {
+          "valueName": "reason",
+          "valueType": "String"
+        }
+      }
+    ]
+  }
+}
diff --git a/...crosoft.Health.Fhir.Ingest.UnitTests/TestInput/data_CodeValueFhirTemplate_Components.json b/...crosoft.Health.Fhir.Ingest.UnitTests/TestInput/data_CodeValueFhirTemplate_Components.json
@@ -42,6 +42,5 @@
         }
       }
     ]
-
   }
 }
diff --git a/test/Microsoft.Health.Fhir.Ingest.UnitTests/TestInput/data_CodeValueFhirTemplate_String.json b/test/Microsoft.Health.Fhir.Ingest.UnitTests/TestInput/data_CodeValueFhirTemplate_String.json
@@ -0,0 +1,11 @@
+{
+  "templateType": "CodeValueFhir",
+  "template": {
+    "periodInterval": 0,
+    "typeName": "stringDetail",
+    "value": {
+      "valueName": "reasonText",
+      "valueType": "String"
+    }
+  }
+}
diff --git a/...emplate/QuanityFhirValueProcessorTests.cs → ...mplate/QuantityFhirValueProcessorTests.cs b/...emplate/QuanityFhirValueProcessorTests.cs → ...mplate/QuantityFhirValueProcessorTests.cs
@@ -1,66 +1,66 @@
-// -------------------------------------------------------------------------------------------------
-// Copyright (c) Microsoft Corporation. All rights reserved.
-// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
-// -------------------------------------------------------------------------------------------------
-
-using System;
-using Hl7.Fhir.Model;
-using Xunit;
-
-namespace Microsoft.Health.Fhir.Ingest.Template
-{
-    public class QuanityFhirValueProcessorTests
-    {
-        [Fact]
-        public void GivenValidTemplate_WhenCreateValue_ThenSampledDataProperlyConfigured_Test()
-        {
-            var processor = new QuantityFhirValueProcessor();
-            var template = new QuantityFhirValueType
-            {
-                Unit = "myUnit",
-                System = "mySystem",
-                Code = "myCode",
-            };
-
-            var data = (DateTime.Now, DateTime.UtcNow, new (DateTime, string)[] { (DateTime.UtcNow, "22.4") });
-            var result = processor.CreateValue(template, data) as Quantity;
-            Assert.NotNull(result);
-            Assert.Equal("myUnit", result.Unit);
-            Assert.Equal("mySystem", result.System);
-            Assert.Equal("myCode", result.Code);
-            Assert.Equal(22.4m, result.Value);
-        }
-
-        [Fact]
-        public void GivenInvalidElementType_WhenMergeValue_ThenNotSupportedExceptionThrown_Test()
-        {
-            var processor = new QuantityFhirValueProcessor();
-            var template = new QuantityFhirValueType();
-            var data = (DateTime.Now, DateTime.UtcNow, new (DateTime, string)[] { (DateTime.UtcNow, "value") });
-
-            Assert.Throws<NotSupportedException>(() => processor.MergeValue(template, data, new FhirDateTime()));
-        }
-
-        [Fact]
-        public void GivenValidTemplate_WhenMergeValue_ThenMergeValueReturned_Test()
-        {
-            var processor = new QuantityFhirValueProcessor();
-            var template = new QuantityFhirValueType
-            {
-                Unit = "myUnit",
-                System = "mySystem",
-                Code = "myCode",
-            };
-
-            var oldQuantity = new Quantity { Value = 1, System = "s", Code = "c", Unit = "u" };
-
-            var data = (DateTime.Now, DateTime.UtcNow, new (DateTime, string)[] { (DateTime.UtcNow, "22.4") });
-            var result = processor.MergeValue(template, data, oldQuantity) as Quantity;
-            Assert.NotNull(result);
-            Assert.Equal("myUnit", result.Unit);
-            Assert.Equal("mySystem", result.System);
-            Assert.Equal("myCode", result.Code);
-            Assert.Equal(22.4m, result.Value);
-        }
-    }
-}
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+
+using System;
+using Hl7.Fhir.Model;
+using Xunit;
+
+namespace Microsoft.Health.Fhir.Ingest.Template
+{
+    public class QuantityFhirValueProcessorTests
+    {
+        [Fact]
+        public void GivenValidTemplate_WhenCreateValue_ThenSampledDataProperlyConfigured_Test()
+        {
+            var processor = new QuantityFhirValueProcessor();
+            var template = new QuantityFhirValueType
+            {
+                Unit = "myUnit",
+                System = "mySystem",
+                Code = "myCode",
+            };
+
+            var data = (DateTime.Now, DateTime.UtcNow, new (DateTime, string)[] { (DateTime.UtcNow, "22.4") });
+            var result = processor.CreateValue(template, data) as Quantity;
+            Assert.NotNull(result);
+            Assert.Equal("myUnit", result.Unit);
+            Assert.Equal("mySystem", result.System);
+            Assert.Equal("myCode", result.Code);
+            Assert.Equal(22.4m, result.Value);
+        }
+
+        [Fact]
+        public void GivenInvalidElementType_WhenMergeValue_ThenNotSupportedExceptionThrown_Test()
+        {
+            var processor = new QuantityFhirValueProcessor();
+            var template = new QuantityFhirValueType();
+            var data = (DateTime.Now, DateTime.UtcNow, new (DateTime, string)[] { (DateTime.UtcNow, "value") });
+
+            Assert.Throws<NotSupportedException>(() => processor.MergeValue(template, data, new FhirDateTime()));
+        }
+
+        [Fact]
+        public void GivenValidTemplate_WhenMergeValue_ThenMergeValueReturned_Test()
+        {
+            var processor = new QuantityFhirValueProcessor();
+            var template = new QuantityFhirValueType
+            {
+                Unit = "myUnit",
+                System = "mySystem",
+                Code = "myCode",
+            };
+
+            var oldQuantity = new Quantity { Value = 1, System = "s", Code = "c", Unit = "u" };
+
+            var data = (DateTime.Now, DateTime.UtcNow, new (DateTime, string)[] { (DateTime.UtcNow, "22.4") });
+            var result = processor.MergeValue(template, data, oldQuantity) as Quantity;
+            Assert.NotNull(result);
+            Assert.Equal("myUnit", result.Unit);
+            Assert.Equal("mySystem", result.System);
+            Assert.Equal("myCode", result.Code);
+            Assert.Equal(22.4m, result.Value);
+        }
+    }
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -42,6 +42,5 @@ @@
             }
           }
         ]
       }
     }