Support Is-a filter in local ValueSet expansion

src/Hl7.Fhir.Conformance/Model/ValueSet.cs

@@ -41,7 +41,7 @@ public bool CodeInExpansion(String code, string? system = null)
                 return null;
         }
 
-        public ValueSet.ContainsComponent FindInExpansion(String code, string? system = null)
+        public ValueSet.ContainsComponent? FindInExpansion(String code, string? system = null)
         {
             ensureExpansion();
 

src/Hl7.Fhir.Conformance/Model/ValueSetExpansionExtensions.cs

@@ -1,16 +1,15 @@
-using Hl7.Fhir.Model;
-using System;
+using System;
 using System.Collections.Generic;
 using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
+
+#nullable enable
 
 namespace Hl7.Fhir.Model
 {
     public static class ValueSetExpansionExtensions
     {
-     
-        public static ValueSet.ContainsComponent FindCode(this IEnumerable<ValueSet.ContainsComponent> cnt, string code, string system=null)
+
+        public static ValueSet.ContainsComponent? FindCode(this IEnumerable<ValueSet.ContainsComponent> cnt, string code, string? system = null)
         {
             foreach (var contains in cnt)
             {
@@ -22,7 +21,7 @@ public static ValueSet.ContainsComponent FindCode(this IEnumerable<ValueSet.Cont
         }
 
 
-        public static ValueSet.ContainsComponent FindCode(this ValueSet.ContainsComponent contains, string code, string system=null)
+        public static ValueSet.ContainsComponent? FindCode(this ValueSet.ContainsComponent contains, string code, string? system = null)
         {
             // Direct hit
             if (code == contains.Code && (system == null || system == contains.System))
@@ -34,20 +33,41 @@ public static ValueSet.ContainsComponent FindCode(this ValueSet.ContainsComponen
             else
                 return null;
         }
+
+        internal static CodeSystem.ConceptDefinitionComponent? FindCode(this IEnumerable<CodeSystem.ConceptDefinitionComponent> concepts, string code)
+        {
+            foreach (var concept in concepts)
+            {
+                var predicate = () => concept.Code == code;
+                var result = concept.findCodeByPredicate(predicate);
+                if (result != null) return result;
+            }
+            return null;
+        }
+
+        private static CodeSystem.ConceptDefinitionComponent? findCodeByPredicate(this IEnumerable<CodeSystem.ConceptDefinitionComponent> concepts, Func<bool> predicate)
+        {
+            foreach (var concept in concepts)
+            {
+                var result = concept.findCodeByPredicate(predicate);
+                if (result != null) return result;
+            }
+            return null;
+        }
+
+        private static CodeSystem.ConceptDefinitionComponent? findCodeByPredicate(this CodeSystem.ConceptDefinitionComponent concept, Func<bool> predicate)
+        {
+            // Direct hit
+            if (predicate.Invoke())
+                return concept;
+
+            // Not in this node, but this node may have child nodes to check
+            if (concept.Concept != null && concept.Concept.Any())
+                return concept.Concept.findCodeByPredicate(predicate);
+            else
+                return null;
+        }
     }
-
-    //public static class ValueSetExtensionExtensions
-    //{
-    //    public const string EXT_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/valueset-deprecated";
-
-    //    public static bool? GetDeprecated(this ValueSet.ConceptDefinitionComponent def)
-    //    {
-    //        return def.GetBoolExtension(EXT_DEPRECATED);
-    //    }
-
-    //    public static void SetDeprecated(this ValueSet.ConceptDefinitionComponent def, bool value)
-    //    {
-    //        def.SetBoolExtension(EXT_DEPRECATED, value);
-    //    }
-    //}
 }
+
+#nullable restore

src/Hl7.Fhir.STU3/Model/ValueSet.cs

@@ -43,7 +43,7 @@ public bool CodeInExpansion(String code, string? system = null)
                 return null;
         }
 
-        public ValueSet.ContainsComponent FindInExpansion(String code, string? system = null)
+        public ValueSet.ContainsComponent? FindInExpansion(String code, string? system = null)
         {
             ensureExpansion();
 

src/Hl7.Fhir.STU3/Model/ValueSetExpansionExtensions.cs

@@ -1,16 +1,15 @@
-using Hl7.Fhir.Model;
-using System;
+using System;
 using System.Collections.Generic;
 using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
+
+#nullable enable
 
 namespace Hl7.Fhir.Model
 {
     public static class ValueSetExpansionExtensions
     {
-     
-        public static ValueSet.ContainsComponent FindCode(this IEnumerable<ValueSet.ContainsComponent> cnt, string code, string system=null)
+
+        public static ValueSet.ContainsComponent? FindCode(this IEnumerable<ValueSet.ContainsComponent> cnt, string code, string? system = null)
         {
             foreach (var contains in cnt)
             {
@@ -22,7 +21,7 @@ public static ValueSet.ContainsComponent FindCode(this IEnumerable<ValueSet.Cont
         }
 
 
-        public static ValueSet.ContainsComponent FindCode(this ValueSet.ContainsComponent contains, string code, string system=null)
+        public static ValueSet.ContainsComponent? FindCode(this ValueSet.ContainsComponent contains, string code, string? system = null)
         {
             // Direct hit
             if (code == contains.Code && (system == null || system == contains.System))
@@ -34,20 +33,68 @@ public static ValueSet.ContainsComponent FindCode(this ValueSet.ContainsComponen
             else
                 return null;
         }
+
+        internal static CodeSystem.ConceptDefinitionComponent? FindCode(this IEnumerable<CodeSystem.ConceptDefinitionComponent> concepts, string code)
+        {
+            foreach (var concept in concepts)
+            {
+                var predicate = () => concept.Code == code;
+                var result = concept.findCodeByPredicate(predicate);
+                if (result != null) return result;
+            }
+            return null;
+        }
+
+        private static CodeSystem.ConceptDefinitionComponent? findCodeByPredicate(this IEnumerable<CodeSystem.ConceptDefinitionComponent> concepts, Func<bool> predicate)
+        {
+            foreach (var concept in concepts)
+            {
+                var result = concept.findCodeByPredicate(predicate);
+                if (result != null) return result;
+            }
+            return null;
+        }
+
+        private static CodeSystem.ConceptDefinitionComponent? findCodeByPredicate(this CodeSystem.ConceptDefinitionComponent concept, Func<bool> predicate)
+        {
+            // Direct hit
+            if (predicate.Invoke())
+                return concept;
+
+            // Not in this node, but this node may have child nodes to check
+            if (concept.Concept != null && concept.Concept.Any())
+                return concept.Concept.findCodeByPredicate(predicate);
+            else
+                return null;
+        }
+
+
+        internal static List<CodeSystem.ConceptDefinitionComponent> FilterCodesByProperty(this IEnumerable<CodeSystem.ConceptDefinitionComponent> concepts, string property, DataType value)
+        {
+            Func<CodeSystem.ConceptDefinitionComponent, bool> predicate = concept => concept.Property.Any(p => p.Code == property && p.Value == value);
+            return concepts.filterCodesByPredicate(predicate);
+        }
+
+
+        private static List<CodeSystem.ConceptDefinitionComponent> filterCodesByPredicate(this IEnumerable<CodeSystem.ConceptDefinitionComponent> concepts, Func<CodeSystem.ConceptDefinitionComponent, bool> predicate)
+        {
+            var result = new List<CodeSystem.ConceptDefinitionComponent>();
+
+            foreach (var concept in concepts)
+            {
+                if (predicate(concept))
+                {
+                    result.Add(concept);
+                }
+
+                if (concept.Concept != null)
+                {
+                    result.AddRange(concept.Concept.filterCodesByPredicate(predicate));
+                }
+            }
+            return result;
+        }
+
+
     }
-
-    //public static class ValueSetExtensionExtensions
-    //{
-    //    public const string EXT_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/valueset-deprecated";
-
-    //    public static bool? GetDeprecated(this ValueSet.ConceptDefinitionComponent def)
-    //    {
-    //        return def.GetBoolExtension(EXT_DEPRECATED);
-    //    }
-
-    //    public static void SetDeprecated(this ValueSet.ConceptDefinitionComponent def, bool value)
-    //    {
-    //        def.SetBoolExtension(EXT_DEPRECATED, value);
-    //    }
-    //}
 }

src/Hl7.Fhir.Shims.Base/Hl7.Fhir.Shims.Base.projitems

@@ -10,6 +10,7 @@
   </PropertyGroup>
   <ItemGroup>
     <Compile Include="$(MSBuildThisFileDirectory)Specification\Source\SnapshotSource.cs" />
+    <Compile Include="$(MSBuildThisFileDirectory)Specification\Terminology\CodeSystemFilterProcessor.cs" />
     <Compile Include="$(MSBuildThisFileDirectory)Specification\Terminology\ExpandParameters.cs" />
     <Compile Include="$(MSBuildThisFileDirectory)Specification\Terminology\ExternalTerminologyService.cs" />
     <Compile Include="$(MSBuildThisFileDirectory)Specification\Terminology\FallbackTerminologyService.cs" />

src/Hl7.Fhir.Shims.Base/Specification/Terminology/CodeSystemFilterProcessor.cs

@@ -0,0 +1,167 @@
+using Hl7.Fhir.Model;
+using Hl7.Fhir.Specification.Source;
+using Hl7.Fhir.Utility;
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.Linq;
+using T = System.Threading.Tasks;
+
+#nullable enable
+
+namespace Hl7.Fhir.Specification.Terminology
+{
+
+    internal static class CodeSystemFilterProcessor
+    {
+        private static readonly ReadOnlyCollection<FilterOperator?> SUPPORTEDFILTERS = new(new List<FilterOperator?> { FilterOperator.IsA });
+        private const string SUBSUMEDBYCODE = "subsumedBy";
+
+        /// <summary>
+        /// Retrieve codes from a CodeSystem resource bases on one or multiple filters.
+        /// </summary>
+        /// <param name="codeSystemUri">Uri of the CodeSystem</param>
+        /// <param name="filters">Filters to be applied</param>
+        /// <param name="settings">ValueSetExpanderSettings </param>
+        /// <returns></returns>
+        /// <exception cref="ValueSetExpansionTooComplexException">Thrown when a filter is applied that is not supported (yet)</exception>
+        /// <exception cref="CodeSystemUnknownException">Thrown when no resource resolver was set in ValueSetExpanderSettings.ValueSetSource</exception>
+        /// <exception cref="CodeSystemUnknownException">Thrown when the requested CodeSystem can not be found by the resource resolver in ValueSetExpanderSettings</exception>
+        internal async static T.Task<IEnumerable<ValueSet.ContainsComponent>> FilterConceptsFromCodeSystem(string codeSystemUri, List<ValueSet.FilterComponent> filters, ValueSetExpanderSettings settings)
+        {
+            if (codeSystemUri == "http://snomed.info/sct" || codeSystemUri == "http://loinc.org")
+            {
+                throw new ValueSetExpansionTooComplexException($"Locally filter codes from Codesystem {codeSystemUri} is not supported");
+            }
+
+            if (filters.Any(f => !SUPPORTEDFILTERS.Contains(f.Op)))
+            {
+                string supportedFiltersString = string.Join(", ", SUPPORTEDFILTERS.Select(f => $"'{f.GetLiteral()}'"));
+                throw new ValueSetExpansionTooComplexException($"ConceptSets with a filter other than {SUPPORTEDFILTERS} are not yet supported.");
+            }
+
+            if (settings.ValueSetSource == null)
+                throw Error.InvalidOperation($"No valueset resolver available to resolve codesystem '{codeSystemUri}', so the expansion cannot be completed.");
+
+            var codeSystem = await settings.ValueSetSource.AsAsync().FindCodeSystemAsync(codeSystemUri).ConfigureAwait(false)
+                  ?? throw new CodeSystemUnknownException($"Cannot find codesystem '{codeSystemUri}', so the defined filter(s) cannot be applied.");
+
+            var result = applyFilters(filters, codeSystem);
+
+            return result.Select(c => c.ToContainsComponent(codeSystem, settings));
+        }
+
+        private static List<CodeSystem.ConceptDefinitionComponent> applyFilters(List<ValueSet.FilterComponent> filters, CodeSystem codeSystem)
+        {
+            var result = new List<CodeSystem.ConceptDefinitionComponent>();
+            var properties = codeSystem.Property;
+            bool first = true;
+
+            foreach (var filter in filters)
+            {
+                //If multiple filters are specified within the include, they SHALL all be true. So the second filter, can just filter the result of the first etc.
+                var newResult = first
+                                    ? applyFilter(codeSystem.Concept, properties, filter)
+                                    : applyFilter(result, properties, filter);
+
+                if (first) first = false;
+                result = newResult.ToList();
+            }
+
+            return result;
+        }
+
+        private static IEnumerable<CodeSystem.ConceptDefinitionComponent> applyFilter(List<CodeSystem.ConceptDefinitionComponent> concepts, List<CodeSystem.PropertyComponent> properties, ValueSet.FilterComponent filter)
+        {
+            return filter.Op switch
+            {
+                FilterOperator.IsA => applyIsAFilter(concepts, properties, filter),
+                _ => throw new InvalidOperationException("no filter was selected")
+            };
+        }
+
+        private static IEnumerable<CodeSystem.ConceptDefinitionComponent> applyIsAFilter(List<CodeSystem.ConceptDefinitionComponent> concepts, List<CodeSystem.PropertyComponent> properties, ValueSet.FilterComponent filter)
+        {
+            var result = new List<CodeSystem.ConceptDefinitionComponent>();
+
+            //find descendants based on subsumedBy
+            if (properties.Any(p => p.Code == SUBSUMEDBYCODE))
+            {
+                //first find the parent itself (if it's in the CodeSystem)
+                if (concepts.FindCode(filter.Value) is { } concept)
+                    result.Add(concept);
+
+                //Create a dictionary which lists children by parent.
+                var dict = new Dictionary<string, List<CodeSystem.ConceptDefinitionComponent>>();
+                addConceptsToSubsumedByDict(concepts, dict);
+
+                //find descendants based on that dictionary
+                var descendants = applySubsumedBy(dict, filter);
+                result.AddRange(descendants);
+            }
+            else
+            {
+                //SubsumedBy is not used, we should only check for a nested hierarchy, and include the code and it's descendants
+                if (concepts.FindCode(filter.Value) is { } concept)
+                    result.Add(concept);
+            }
+            return result;
+        }
+
+        private static void addConceptsToSubsumedByDict(List<CodeSystem.ConceptDefinitionComponent> concepts, Dictionary<string, List<CodeSystem.ConceptDefinitionComponent>> dict)
+        {
+            foreach (var concept in concepts)
+            {
+                //find all properties that are parents.
+                var parents = concept.Property
+                                       .Where(p => p.Code == SUBSUMEDBYCODE && p.Value is Code && ((Code)p.Value).Value is not null)
+                                       .Select(p => ((Code)p.Value).Value);
+
+                //Find all their children
+                foreach (var parent in parents)
+                {
+                    if (dict.ContainsKey(parent))
+                    {
+                        dict[parent].Add(concept);
+                    }
+                    else
+                    {
+                        dict.Add(parent, new List<CodeSystem.ConceptDefinitionComponent> { concept });
+                    }
+                }
+
+                if (concept.Concept is not null && concept.Concept.Any())
+                {
+                    addConceptsToSubsumedByDict(concept.Concept, dict);
+                }
+            }
+        }
+
+        private static List<CodeSystem.ConceptDefinitionComponent> applySubsumedBy(Dictionary<string, List<CodeSystem.ConceptDefinitionComponent>> dict, ValueSet.FilterComponent filter)
+        {
+            var result = new List<CodeSystem.ConceptDefinitionComponent>();
+            var root = filter.Value;
+            if (root != null)
+            {
+                addDescendants(dict, root, result);
+            }
+            return result;
+        }
+
+        //recursively loop through all the children to eventually find all descendants.
+        private static void addDescendants(Dictionary<string, List<CodeSystem.ConceptDefinitionComponent>> dict, string parent, List<CodeSystem.ConceptDefinitionComponent> result)
+        {
+            if (dict.TryGetValue(parent, out var descendants))
+            {
+                foreach (var descendant in descendants)
+                {
+                    result.Add(descendant);
+                    parent = descendant.Code;
+                    addDescendants(dict, parent, result);
+                }
+            }
+        }
+    }
+}
+
+#nullable restore