Adding some UT/E2E test for $includes operation.

src/Microsoft.Health.Fhir.Api/Features/Routing/UrlResolver.cs

@@ -368,27 +368,22 @@ private Uri GetRouteUri(HttpContext httpContext, string routeName, RouteValueDic
                     pathBase += "/";
                 }
 
-                if (address == null)
-                {
-                    uriString = _linkGenerator.GetUriByRouteValues(
+                uriString = address == null ?
+                    _linkGenerator.GetUriByRouteValues(
                         httpContext,
                         routeName,
                         routeValues,
                         scheme,
                         new HostString(host),
-                        pathBase);
-                }
-                else
-                {
-                    uriString = _linkGenerator.GetUriByAddress<RouteValuesAddress>(
+                        pathBase) :
+                    _linkGenerator.GetUriByAddress<RouteValuesAddress>(
                         httpContext,
                         address,
                         address.ExplicitValues,
                         address.AmbientValues,
                         scheme,
                         new HostString(host),
                         pathBase);
-                }
             }
 
             return new Uri(uriString);

src/Microsoft.Health.Fhir.Core/Features/KnownQueryParameterNames.cs

@@ -127,8 +127,13 @@ public static class KnownQueryParameterNames
         public const string MaxCount = "_maxCount";
 
         /// <summary>
-        /// The include continuation token parameter.
+        /// The $includes continuation token parameter.
         /// </summary>
         public const string IncludesContinuationToken = "includesCt";
+
+        /// <summary>
+        /// The $includes count parameter.
+        /// </summary>
+        public const string IncludesCount = "_includesCount";
     }
 }

src/Microsoft.Health.Fhir.Core/Models/KnownResourceTypes.cs

@@ -67,6 +67,10 @@ public static class KnownResourceTypes
 
         public const string CareTeam = "CareTeam";
 
+        public const string MedicationDispense = "MedicationDispense";
+
+        public const string MedicationRequest = "MedicationRequest";
+
         public const string All = "all";
     }
 }

src/Microsoft.Health.Fhir.Core/Resources.resx

@@ -764,8 +764,16 @@
     <value>The number of included results exceeded the limit of {0}</value>
     <comment>{0} is the limit of how many include results the service will return.</comment>
   </data>
-</root>
   <data name="UnsupportedIncludesOperation" xml:space="preserve">
-    <value>The '$includes' operation is not supported for CosmosDB data store.</value>
+    <value>The '$includes' operation is not supported.</value>
   </data>
-</root>
+  <data name="SearchParamaterIncludesCountExceedLimit" xml:space="preserve">
+    <value>The '_includesCount' parameter exceeds limit configured for server. Current limit is {0} while the `_includesCount` parameter set to {1}.</value>
+  </data>
+  <data name="InvalidSearchIncludesCountSpecified" xml:space="preserve">
+    <value>The '_includesCount' parameter value must be an integer greater than zero.</value>
+  </data>
+  <data name="MissingIncludesContinuationToken" xml:space="preserve">
+    <value>"The 'includesCt' parameter must be provided for the $includes operation."</value>
+  </data>
+</root>

src/Microsoft.Health.Fhir.Shared.Core.UnitTests/Features/Search/BundleFactoryTests.cs

@@ -38,6 +38,7 @@ public class BundleFactoryTests
         private readonly BundleFactory _bundleFactory;
 
         private const string _continuationToken = "ct";
+        private const string _includesContinuationToken = "includesCt";
         private const string _resourceUrlFormat = "http://resource/{0}";
         private static readonly string _correlationId = Guid.NewGuid().ToString();
         private static readonly Uri _selfUrl = new Uri("http://self/");
@@ -224,5 +225,44 @@ public void GivenAHistoryResultWithAllHttpVerbs_WhenCreateHistoryBundle_ThenBund
                 Assert.NotNull(actual.ToPoco<Bundle>().Entry[0].Response.Status);
             }
         }
+
+        [Theory]
+        [InlineData(RouteNames.SearchResources, _includesContinuationToken)]
+        [InlineData(RouteNames.Includes, _includesContinuationToken)]
+        [InlineData(RouteNames.SearchResources, null)]
+        [InlineData(RouteNames.Includes, null)]
+        public void GivenASearchResultWithIncludesContinuationToken_WhenCreateSearchBundle_ThenCorrectBundleShouldBeReturned(string routeName, string includesContinuationToken)
+        {
+            _fhirRequestContextAccessor.RequestContext.RouteName = routeName;
+
+            var encodedContinuationToken = ContinuationTokenEncoder.Encode(_continuationToken);
+            _urlResolver.ResolveRouteUrl(_unsupportedSearchParameters, null, encodedContinuationToken, true).Returns(_nextUrl);
+            _urlResolver.ResolveRouteUrl(_unsupportedSearchParameters).Returns(_selfUrl);
+
+            var includesUrl = "https://localhost/Patient/$include";
+            var encodedIncludesContinuationToken = includesContinuationToken != null ? ContinuationTokenEncoder.Encode(includesContinuationToken) : null;
+            _urlResolver.ResolveRouteUrl(
+                Arg.Any<IReadOnlyCollection<Tuple<string, string>>>(),
+                Arg.Any<IReadOnlyList<(SearchParameterInfo searchParameterInfo, SortOrder sortOrder)>>(),
+                Arg.Is<string>(x => x == null),
+                Arg.Any<bool>(),
+                Arg.Is<string>(x => x == encodedIncludesContinuationToken),
+                Arg.Any<string>(),
+                Arg.Any<IDictionary<string, object>>()).Returns(new Uri(includesUrl));
+
+            var searchResult = new SearchResult(new SearchResultEntry[0], _continuationToken, null, _unsupportedSearchParameters, null, includesContinuationToken);
+            var actual = _bundleFactory.CreateSearchBundle(searchResult);
+
+            if (routeName != RouteNames.Includes)
+            {
+                Assert.Equal(_nextUrl.OriginalString, actual.Scalar<string>("Bundle.link.where(relation='next').url"));
+                Assert.Equal(includesContinuationToken != null ? includesUrl : null, actual.Scalar<string>("Bundle.link.where(relation='related').url"));
+            }
+            else
+            {
+                Assert.Equal(includesContinuationToken != null ? includesUrl : null, actual.Scalar<string>("Bundle.link.where(relation='next').url"));
+                Assert.Null(actual.Scalar<string>("Bundle.link.where(relation='related').url"));
+            }
+        }
     }
 }

src/Microsoft.Health.Fhir.Shared.Core/Features/Search/BundleFactory.cs

@@ -190,7 +190,7 @@ private void CreateLinks(SearchResult result, Bundle bundle)
                             new Bundle.LinkComponent()
                             {
                                 Relation = "related",
-                                Url = url.AbsoluteUri,
+                                Url = url?.AbsoluteUri,
                             });
                     }
                     catch (UriFormatException)

src/Microsoft.Health.Fhir.Shared.Core/Features/Search/SearchOptionsFactory.cs

@@ -119,9 +119,12 @@ public SearchOptions Create(
             searchOptions.IgnoreSearchParamHash = queryParameters != null && queryParameters.Any(_ => _.Item1 == KnownQueryParameterNames.IgnoreSearchParamHash && _.Item2 != null);
 
             string continuationToken = null;
-            string includesContinuationToken = null;
             string feedRange = null;
 
+            // $includes related parameters
+            string includesContinuationToken = null;
+            int? includesCount = null;
+
             var searchParams = new SearchParams();
             var unsupportedSearchParameters = new List<Tuple<string, string>>();
             bool setDefaultBundleTotal = true;
@@ -229,15 +232,20 @@ public SearchOptions Create(
                             string.Format(Core.Resources.MultipleQueryParametersNotAllowed, KnownQueryParameterNames.IncludesContinuationToken));
                     }
 
-                    if (!isIncludesOperation)
-                    {
-                        // TODO: should this case be ignored or throw an exception? The Hl7 doc says, we should ignore it in general. (https://www.hl7.org/fhir/R4/search.html#errors)
-                        // throw new BadRequestException(string.Format(Core.Resources.InvalidContinuationToken, query.Item2, SupportedTotalTypes));
-                    }
-
                     includesContinuationToken = ContinuationTokenEncoder.Decode(query.Item2);
                     setDefaultBundleTotal = false;
                 }
+                else if (string.Equals(query.Item1, KnownQueryParameterNames.IncludesCount, StringComparison.OrdinalIgnoreCase))
+                {
+                    if (int.TryParse(query.Item2, out int count) && count > 0)
+                    {
+                        includesCount = count;
+                    }
+                    else
+                    {
+                        throw new BadRequestException(Core.Resources.InvalidSearchIncludesCountSpecified);
+                    }
+                }
                 else
                 {
                     // Parse the search parameters.
@@ -255,7 +263,7 @@ public SearchOptions Create(
 
             if (isIncludesOperation && string.IsNullOrEmpty(includesContinuationToken))
             {
-                throw new BadRequestException("'includesCt' parameter must be provided for $includes operation.");
+                throw new BadRequestException(Core.Resources.MissingIncludesContinuationToken);
             }
 
             searchOptions.ContinuationToken = continuationToken;
@@ -301,7 +309,23 @@ public SearchOptions Create(
                 searchOptions.MaxItemCount = _featureConfiguration.DefaultItemCountPerSearch;
             }
 
-            searchOptions.IncludeCount = _featureConfiguration.DefaultIncludeCountPerSearch;
+            if (includesCount.HasValue && includesCount <= _featureConfiguration.DefaultIncludeCountPerSearch)
+            {
+                searchOptions.IncludeCount = includesCount.Value;
+            }
+            else
+            {
+                if (includesCount.HasValue)
+                {
+                    _contextAccessor.RequestContext?.BundleIssues.Add(
+                        new OperationOutcomeIssue(
+                            OperationOutcomeConstants.IssueSeverity.Information,
+                            OperationOutcomeConstants.IssueType.Informational,
+                            string.Format(Core.Resources.SearchParamaterIncludesCountExceedLimit, _featureConfiguration.DefaultIncludeCountPerSearch, includesCount)));
+                }
+
+                searchOptions.IncludeCount = _featureConfiguration.DefaultIncludeCountPerSearch;
+            }
 
             if (searchParams.Elements?.Any() == true && searchParams.Summary != null && searchParams.Summary != SummaryType.False)
             {

src/Microsoft.Health.Fhir.SqlServer/Features/Search/Expressions/Visitors/IncludeRewriter.cs

@@ -18,8 +18,8 @@ internal class IncludeRewriter : SqlExpressionRewriterWithInitialContext<object>
     {
         internal static readonly IncludeRewriter Instance = new IncludeRewriter();
 
-        private static readonly SearchParamTableExpression IncludeUnionAllExpression = new SearchParamTableExpression(null, null, SearchParamTableExpressionKind.IncludeUnionAll);
-        private static readonly SearchParamTableExpression IncludeLimitExpression = new SearchParamTableExpression(null, null, SearchParamTableExpressionKind.IncludeLimit);
+        protected static readonly SearchParamTableExpression IncludeUnionAllExpression = new SearchParamTableExpression(null, null, SearchParamTableExpressionKind.IncludeUnionAll);
+        protected static readonly SearchParamTableExpression IncludeLimitExpression = new SearchParamTableExpression(null, null, SearchParamTableExpressionKind.IncludeLimit);
 
         public override Expression VisitSqlRoot(SqlRootExpression expression, object context)
         {
@@ -63,7 +63,7 @@ public override Expression VisitSqlRoot(SqlRootExpression expression, object con
             return new SqlRootExpression(reorderedExpressions, expression.ResourceTableExpressions);
         }
 
-        private static List<SearchParamTableExpression> SortIncludeIterateExpressions(List<SearchParamTableExpression> expressions)
+        protected static List<SearchParamTableExpression> SortIncludeIterateExpressions(List<SearchParamTableExpression> expressions)
         {
             // Based on Khan's algorithm. See https://en.wikipedia.org/wiki/Topological_sorting.
             // The search queries are acyclic.

src/Microsoft.Health.Fhir.SqlServer/Features/Search/Expressions/Visitors/IncludesOperationRewriter.cs

@@ -10,19 +10,9 @@
 
 namespace Microsoft.Health.Fhir.SqlServer.Features.Search.Expressions.Visitors
 {
-    internal class IncludesOperationRewriter : SqlExpressionRewriterWithInitialContext<object>
+    internal class IncludesOperationRewriter : IncludeRewriter
     {
-        internal static readonly IncludesOperationRewriter Instance = new IncludesOperationRewriter();
-
-        private static readonly SearchParamTableExpression IncludeLimitExpression = new SearchParamTableExpression(
-            null,
-            null,
-            SearchParamTableExpressionKind.IncludeLimit);
-
-        private static readonly SearchParamTableExpression IncludeUnionAllExpression = new SearchParamTableExpression(
-            null,
-            null,
-            SearchParamTableExpressionKind.IncludeUnionAll);
+        internal static new readonly IncludesOperationRewriter Instance = new IncludesOperationRewriter();
 
         public override Expression VisitSqlRoot(SqlRootExpression expression, object context)
         {
@@ -51,10 +41,5 @@ public override Expression VisitSqlRoot(SqlRootExpression expression, object con
             var reorderedExpressions = nonIncludeExpressions.Concat(sortedIncludeExpressions).Concat(new[] { IncludeUnionAllExpression, IncludeLimitExpression }).ToList();
             return new SqlRootExpression(reorderedExpressions, expression.ResourceTableExpressions);
         }
-
-        private IEnumerable<SearchParamTableExpression> SortIncludeIterateExpressions(List<SearchParamTableExpression> includeIterateExpressions)
-        {
-            throw new NotImplementedException();
-        }
     }
 }

src/Microsoft.Health.Fhir.SqlServer/Features/Search/Expressions/Visitors/QueryGenerators/SqlQueryGenerator.cs

@@ -781,12 +781,8 @@ private void HandleTableKindInclude(
 
             StringBuilder.Append("SELECT DISTINCT ");
 
-            if (includeExpression.Reversed || context.IsIncludesOperation)
-            {
-                // In case its revinclude, we limit the number of returned items as the resultset size is potentially
-                // unbounded. we ask for +1 so in the limit expression we know if to mark at truncated...
-                StringBuilder.Append("TOP (").Append(Parameters.AddParameter(context.IncludeCount + 1, includeInHash: false)).Append(") ");
-            }
+            // Adding 1 to the include count for detecting a case of truncated "include" resources.
+            StringBuilder.Append("TOP (").Append(Parameters.AddParameter(context.IncludeCount + 1, includeInHash: false)).Append(") ");
 
             var table = !includeExpression.Reversed ? referenceTargetResourceTableAlias : referenceSourceTableAlias;
 
@@ -911,6 +907,7 @@ private void HandleTableKindInclude(
                 {
                     var tableAlias = includeExpression.Reversed ? referenceSourceTableAlias : referenceTargetResourceTableAlias;
                     delimited.BeginDelimitedElement()
+                        .Append("(")
                         .Append(VLatest.Resource.ResourceTypeId, tableAlias)
                         .Append(" > ")
                         .Append(includesContinuationToken.IncludeResourceTypeId)
@@ -922,7 +919,7 @@ private void HandleTableKindInclude(
                         .Append(VLatest.ReferenceSearchParam.ResourceSurrogateId, tableAlias)
                         .Append(" > ")
                         .Append(includesContinuationToken.IncludeResourceSurrogateId)
-                        .Append(")");
+                        .Append("))");
                 }
 
                 var scope = delimited.BeginDelimitedElement();
@@ -996,15 +993,8 @@ private void HandleTableKindInclude(
 
         private void HandleTableKindIncludeLimit(SearchOptions context)
         {
-            var includeCount = context.IncludeCount;
-            if (context.IsIncludesOperation)
-            {
-                // Adding 1 for detecting an IsPartial resource if any.
-                includeCount++;
-            }
-
             StringBuilder.Append("SELECT DISTINCT TOP (")
-                .Append(Parameters.AddParameter(includeCount, includeInHash: false))
+                .Append(Parameters.AddParameter(context.IncludeCount + 1, includeInHash: false))
                 .Append(") T1, Sid1, IsMatch, ");
 
             StringBuilder.Append("CASE WHEN count_big(*) over() > ")

src/Microsoft.Health.Fhir.Tests.Common/Microsoft.Health.Fhir.Tests.Common.csproj

@@ -66,6 +66,7 @@
     <EmbeddedResource Include="TestFiles\Normative\Import-DupPatientTemplate.ndjson" />
     <EmbeddedResource Include="TestFiles\Normative\Import-Patient.ndjson" />
     <EmbeddedResource Include="TestFiles\Normative\Import-SinglePatientTemplate.ndjson" />
+    <EmbeddedResource Include="TestFiles\Normative\Includes-TestResources.json" />
     <EmbeddedResource Include="TestFiles\Normative\Medication.json" />
     <EmbeddedResource Include="TestFiles\Normative\MemberMatch.json" />
     <EmbeddedResource Include="TestFiles\Normative\PatientWithUnknownElements.json" />
@@ -206,6 +207,7 @@
     <EmbeddedResource Include="TestFiles\R5\DocumentReference-example-with-base64.json" />
     <EmbeddedResource Include="TestFiles\R5\Encounter-For-Patient-f001.json" />
     <EmbeddedResource Include="TestFiles\R5\Immunization.json" />
+    <EmbeddedResource Include="TestFiles\R5\Includes-TestResources.json" />
     <EmbeddedResource Include="TestFiles\R5\InvalidCompartmentDefinition.json" />
     <EmbeddedResource Include="TestFiles\R5\Location-example-hq.json" />
     <EmbeddedResource Include="TestFiles\R5\MedicinalProductDefinition.json" />