fix: specimen source handling

data/Templates/eCR/Entry/Result/_entry.liquid

@@ -16,16 +16,17 @@
         {% include 'Reference/DiagnosticReport/Performer' ID: diagnosticId, REF: fullPerformerId -%}
         {% endif -%}
     {% endif -%}
+    {% assign collectTime = null %}
     {% if entry.organizer.effectiveTime.low and entry.organizer.effectiveTime.low.value -%}
         {% assign collectTime = entry.organizer.effectiveTime.low.value -%}
     {% elsif entry.organizer.effectiveTime.high and entry.organizer.effectiveTime.high.value -%}
         {% assign collectTime = entry.organizer.effectiveTime.high.value -%}
     {% elsif entry.organizer.effectiveTime and entry.organizer.effectiveTime.value and entry.organizer.effectiveTime.value != "UNK"-%}
         {% assign collectTime = entry.organizer.effectiveTime.value -%}
-    {% else -%}
-        {% assign collectTime = "None" -%}
     {% endif -%}
 
+    {% assign specValue = null %}
+    {% assign receiveTime = null %}
     {% assign comps = entry.organizer.component | to_array -%}
     {% for comp in comps -%}
         {% if comp.procedure  -%}
@@ -50,15 +51,15 @@
                     {% assign specValue = playingEntity.code.originalText._ -%}
                 {% elsif playingEntity.code.displayName -%}
                      {% assign specValue = playingEntity.code.displayName -%}
-                {% else -%}
-                    {% assign specValue = "None" -%}
                 {% endif -%}
-            {% else  -%}
-                {% assign specValue = "None" -%}
             {% endif -%}
         {% endif -%}
-    {% endfor-%}   
+    {% endfor -%}   
     {% for component in comps %}
-        {% include 'Entry/Result/entry_organizer_component' with component, text: text %}
+        {% include 'Entry/Result/entry_organizer_component' with component, text: text, specValue: specValue, collectTime: collectTime, receiveTime: receiveTime, diagnosticId: diagnosticId %}
     {% endfor %}
 {% endif -%}
+{% comment %} Prevent weird variable leakage {% endcomment %}
+{% assign specValue = null %}
+{% assign receiveTime = null %}
+{% assign collectTime = null %}

data/Templates/eCR/Resource/_Observation.liquid

@@ -140,23 +140,23 @@
         {% assign observationValueReferenceValue = observationEntry.value.reference.value -%}
         "extension":
             [ {
-                {% if specimenValue and specimenValue != "None" or collectTime and collectTime != "None" or observationTextReferenceValue != "None" or observationValueReferenceValue != "None" -%}
+                {% if specimenValue != null or collectTime != null or receiveTime != null -%}
 
                     "url" : "http://hl7.org/fhir/R4/specimen.html",
                     "extension": [
-                    {% if specimenValue and specimenValue != "None" -%}
+                    {% if specimenValue != null -%}
                         {
                             "url" : "specimen source",
                             "valueString" : "{{ specimenValue }}",
                         },
                     {% endif -%}
-                    {% if collectTime and collectTime != "None" -%}
+                    {% if collectTime != null -%}
                         {
                             "url" : "specimen collection time",
                             "valueDateTime" : "{{ collectTime | format_as_date_time }}",
                         },
                     {% endif -%}
-                    {% if receiveTime and receiveTime != "None" -%}
+                    {% if receiveTime != null -%}
                         {
                             "url" : "specimen receive time",
                             "valueDateTime" : "{{ receiveTime | format_as_date_time }}",

src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/BaseConvertDataFunctionalTests.cs

@@ -3,6 +3,7 @@
 // Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 // -------------------------------------------------------------------------------------------------
 
+using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
@@ -213,6 +214,20 @@ public static IEnumerable<object[]> GetDataForCcda()
             });
         }
 
+        public static IEnumerable<object[]> GetDataForEcr()
+        {
+            var data = new List<string[]>
+            {
+                new[] { @"EICR", @"eCR_full.xml", @"eCR_full-expected.json" },
+            };
+            return data.Select(item => new[]
+            {
+                item[0],
+                Path.Join(Constants.SampleDataDirectory, "eCR", item[1]),
+                Path.Join(Constants.ExpectedDataFolder, "eCR", item[0], item[2]),
+            });
+        }
+
         public static IEnumerable<object[]> GetDataForJson()
         {
             var data = new List<string[]>
@@ -332,8 +347,17 @@ protected void ConvertCCDAMessageAndValidateExpectedResponse(ITemplateProvider t
             var actualObject = JObject.Parse(actualContent);
 
             // Remove DocumentReference, where date is different every time conversion is run and gzip result is OS dependent
-            expectedObject["entry"]?.Last()?.Remove();
-            actualObject["entry"]?.Last()?.Remove();
+            if (expectedObject["entry"]?.Last()["resource"]["resourceType"].ToString() == "DocumentReference")
+            {
+                expectedObject["entry"]?.Last()?.Remove();
+                actualObject["entry"]?.Last()?.Remove();
+            }
+
+            var diff = DiffHelper.FindDiff(actualObject, expectedObject);
+            if (diff.HasValues)
+            {
+                Console.WriteLine(diff);
+            }
 
             Assert.True(JToken.DeepEquals(expectedObject, actualObject));
         }

src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/ConvertDataTemplateDirectoryProviderFunctionalTests.cs

@@ -88,6 +88,16 @@ public void GivenCcdaDocument_WhenConverting_ExpectedFhirResourceShouldBeReturne
             ConvertCCDAMessageAndValidateExpectedResponse(templateProvider, rootTemplate, inputFile, expectedFile);
         }
 
+        [Theory]
+        [MemberData(nameof(GetDataForEcr))]
+        public void GivenEcrDocument_WhenConverting_ExpectedFhirResourceShouldBeReturned(string rootTemplate, string inputFile, string expectedFile)
+        {
+            var templateDirectory = Path.Join(AppDomain.CurrentDomain.BaseDirectory, Constants.TemplateDirectory, "eCR");
+            var templateProvider = new TemplateProvider(templateDirectory, DataType.Ccda);
+
+            ConvertCCDAMessageAndValidateExpectedResponse(templateProvider, rootTemplate, inputFile, expectedFile);
+        }
+
         [Theory]
         [MemberData(nameof(GetDataForStu3ToR4))]
         public void GivenStu3FhirData_WhenConverting_ExpectedR4FhirResourceShouldBeReturned(string rootTemplate, string inputFile, string expectedFile)

src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs

@@ -0,0 +1,64 @@
+using System.Linq;
+using Newtonsoft.Json.Linq;
+
+namespace Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests
+{
+    // from https://stackoverflow.com/questions/24876082/find-and-return-json-differences-using-newtonsoft-in-c
+    public static class DiffHelper
+    {
+        public static JObject FindDiff(this JToken Current, JToken Model)
+        {
+            var diff = new JObject();
+            if (JToken.DeepEquals(Current, Model)) return diff;
+
+            switch(Current.Type)
+            {
+                case JTokenType.Object:
+                    {
+                        var current = Current as JObject;
+                        var model = Model as JObject;
+                        var addedKeys = current.Properties().Select(c => c.Name).Except(model.Properties().Select(c => c.Name));
+                        var removedKeys = model.Properties().Select(c => c.Name).Except(current.Properties().Select(c => c.Name));
+                        var unchangedKeys = current.Properties().Where(c => JToken.DeepEquals(c.Value, Model[c.Name])).Select(c => c.Name);
+                        foreach (var k in addedKeys)
+                        {
+                            diff[k] = new JObject
+                            {
+                                ["+"] = Current[k]
+                            };
+                        }
+                        foreach (var k in removedKeys)
+                        {
+                            diff[k] = new JObject
+                            {
+                                ["-"] = Model[k]
+                            };
+                        }
+                        var potentiallyModifiedKeys = current.Properties().Select(c => c.Name).Except(addedKeys).Except(unchangedKeys);
+                        foreach (var k in potentiallyModifiedKeys)
+                        {
+                            var foundDiff = FindDiff(current[k], model[k]);
+                            if(foundDiff.HasValues) diff[k] = foundDiff;
+                        }
+                    }
+                    break;
+                case JTokenType.Array:
+                    {
+                        var current = Current as JArray;
+                        var model = Model as JArray;
+                        var plus = new JArray(current.Except(model, new JTokenEqualityComparer()));
+                        var minus = new JArray(model.Except(current, new JTokenEqualityComparer()));
+                        if (plus.HasValues) diff["+"] = plus;
+                        if (minus.HasValues) diff["-"] = minus;
+                    }
+                    break;
+                default:
+                    diff["+"] = Current;
+                    diff["-"] = Model;
+                    break;
+            }
+
+            return diff;
+        }
+    }
+}