fix: #1294: Streaming Genotype matcher response to prevent memory exc…

…eptions.
Anthony-Nolan · May 2, 2024 · f544488 · f544488
1 parent 00583ce
commit f544488
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Showing 4 changed files with 63 additions and 39 deletions.
diff --git a/Atlas.MatchPrediction.Functions/Functions/Debug/MatchCalculationFunctions.cs b/Atlas.MatchPrediction.Functions/Functions/Debug/MatchCalculationFunctions.cs
@@ -49,15 +49,15 @@ public class MatchCalculationFunctions
                 MatchPredictionParameters = input.MatchPredictionParameters
             });
 
-            var response = new GenotypeMatcherResponse
+            var matcherResponse = new GenotypeMatcherResponse
             {
                 MatchPredictionParameters = input.MatchPredictionParameters,
                 PatientInfo = BuildSubjectResult(result.PatientResult, frequencySet.PatientSet, input.Patient),
                 DonorInfo = BuildSubjectResult(result.DonorResult, frequencySet.DonorSet, input.Donor),
-                MatchedGenotypePairs = result.GenotypeMatchDetails.ToSingleDelimitedString()
+                MatchedGenotypePairs = result.GenotypeMatchDetails.ToFormattedStrings(),
             };
 
-            return new JsonResult(response);
+            return await StreamGenotypeMatcherResponse(request, matcherResponse);
         }
 
         private static SubjectResult BuildSubjectResult(
@@ -72,5 +72,41 @@ public class MatchCalculationFunctions
                 set, 
                 subjectInfo.HlaTyping.ToPhenotypeInfo().PrettyPrint());
         }
+
+        /// <summary>
+        /// <paramref name="matcherResponse"/> can be very large. Streaming to avoid memory issues.
+        /// </summary>
+        private static async Task<IActionResult> StreamGenotypeMatcherResponse(HttpRequest request, GenotypeMatcherResponse matcherResponse)
+        {
+            request.HttpContext.Response.ContentType = "application/json";
+            await using var writer = new StreamWriter(request.HttpContext.Response.Body);
+            await using var jsonWriter = new JsonTextWriter(writer);
+
+            await jsonWriter.WriteStartObjectAsync();
+
+            await jsonWriter.WritePropertyNameAsync($"{nameof(matcherResponse.MatchPredictionParameters)}");
+            await jsonWriter.WriteValueAsync(JsonConvert.SerializeObject(matcherResponse.MatchPredictionParameters));
+
+            await jsonWriter.WritePropertyNameAsync($"{nameof(matcherResponse.PatientInfo)}");
+            await jsonWriter.WriteValueAsync(JsonConvert.SerializeObject(matcherResponse.PatientInfo));
+
+            await jsonWriter.WritePropertyNameAsync($"{nameof(matcherResponse.DonorInfo)}");
+            await jsonWriter.WriteValueAsync(JsonConvert.SerializeObject(matcherResponse.DonorInfo));
+
+            await jsonWriter.WritePropertyNameAsync($"{nameof(matcherResponse.MatchedGenotypePairs)}");
+            await jsonWriter.WriteStartArrayAsync();
+            foreach (var pair in matcherResponse.MatchedGenotypePairs)
+            {
+                await jsonWriter.WriteValueAsync(JsonConvert.SerializeObject(pair));
+            }
+            await jsonWriter.WriteEndArrayAsync();
+
+            await jsonWriter.WriteEndObjectAsync();
+
+            await writer.FlushAsync();
+
+            // Required to avoid the host trying to add headers to the response
+            return new EmptyResult();
+        }
     }
 }
diff --git a/Atlas.MatchPrediction.Functions/Models/Debug/GenotypeMatcherResponse.cs b/Atlas.MatchPrediction.Functions/Models/Debug/GenotypeMatcherResponse.cs
@@ -1,4 +1,5 @@
-using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
+using System.Collections.Generic;
+using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
 using Atlas.MatchPrediction.Models;
 
 namespace Atlas.MatchPrediction.Functions.Models.Debug
@@ -10,9 +11,9 @@ public class GenotypeMatcherResponse
         public SubjectResult DonorInfo { get; set; }
 
         /// <summary>
-        /// Patient-donor genotype pairs (represented as a single, formatted string) and their match counts.
+        /// Patient-donor genotype pairs and their match counts.
         /// </summary>
-        public string MatchedGenotypePairs { get; set; }
+        public IEnumerable<string> MatchedGenotypePairs { get; set; }
     }
 
     public class SubjectResult

diff --git a/Atlas.MatchPrediction.Functions/Services/Debug/GenotypeLikelihoodFormatter.cs b/Atlas.MatchPrediction.Functions/Services/Debug/GenotypeLikelihoodFormatter.cs
@@ -24,48 +24,35 @@ public static string ToSingleDelimitedString(this Dictionary<PhenotypeInfo<strin
             return builder.ToString();
         }
 
-        public static string ToSingleDelimitedString(this IEnumerable<GenotypeMatchDetails> genotypeMatchDetails)
+        /// <summary>
+        /// Converts a collection of GenotypeMatchDetails to a collection of formatted strings.
+        /// Uses yield return to avoid creating a large collection in memory.
+        /// </summary>
+        public static IEnumerable<string> ToFormattedStrings(this IEnumerable<GenotypeMatchDetails> genotypeMatchDetails)
         {
             // ReSharper disable once PossibleMultipleEnumeration - `IsNullOrEmpty` extension method does not enumerate full collection
             if (genotypeMatchDetails.IsNullOrEmpty())
             {
-                return "No available genotype match details.";
+                yield return "No available genotype match details.";
             }
 
-            var builder = new StringBuilder();
-
-            var genotypePairs = BuildGenotypePairsWithMatchCounts(genotypeMatchDetails);
+            yield return $"Total{FieldDelimiter}" +
+                         $"A{FieldDelimiter}" +
+                         $"B{FieldDelimiter}" +
+                         $"C{FieldDelimiter}" +
+                         $"DQB1{FieldDelimiter}" +
+                         $"DRB1{FieldDelimiter}" +
+                         $"{BuildGenotypeLikelihoodHeader("P-")}{FieldDelimiter}" +
+                         $"{BuildGenotypeLikelihoodHeader("D-")}";
 
-            foreach (var pair in genotypePairs)
+            // ReSharper disable once PossibleMultipleEnumeration
+            foreach (var details in genotypeMatchDetails.OrderByDescending(x => x.MatchCount))
             {
-                builder.AppendLine(pair);
+                yield return $"{BuildCounts(details.MatchCount, details.MatchCounts)}{FieldDelimiter}" +
+                             $"{details.PatientGenotype.ToDelimitedString(details.PatientGenotypeLikelihood)}{FieldDelimiter}" +
+                             $"{details.DonorGenotype.ToDelimitedString(details.DonorGenotypeLikelihood)}";
             }
 
-            return builder.ToString();
-        }
-
-        private static IEnumerable<string> BuildGenotypePairsWithMatchCounts(IEnumerable<GenotypeMatchDetails> genotypeMatchDetails)
-        {
-            var header =  $"Total{FieldDelimiter}" +
-                                $"A{FieldDelimiter}" +
-                                $"B{FieldDelimiter}" +
-                                $"C{FieldDelimiter}" +
-                                $"DQB1{FieldDelimiter}" +
-                                $"DRB1{FieldDelimiter}" +
-                                $"{BuildGenotypeLikelihoodHeader("P-")}{FieldDelimiter}" +
-                                $"{BuildGenotypeLikelihoodHeader("D-")}";
-
-            var formattedStrings = new List<string> { header };
-            formattedStrings.AddRange(
-                genotypeMatchDetails
-                .OrderByDescending(x => x.MatchCount)
-                .Select(x =>
-                    $"{BuildCounts(x.MatchCount, x.MatchCounts)}{FieldDelimiter}" +
-                    $"{x.PatientGenotype.ToDelimitedString(x.PatientGenotypeLikelihood)}{FieldDelimiter}" +
-                    $"{x.DonorGenotype.ToDelimitedString(x.DonorGenotypeLikelihood)}"));
-
-            return formattedStrings;
-
             string BuildCounts(int totalCount, LociInfo<int?> locusCounts) =>
                 $"{totalCount}{FieldDelimiter}" +
                 $"{locusCounts.A}{FieldDelimiter}" +

diff --git a/Atlas.MatchPrediction/Models/GenotypeMatchDetails.cs b/Atlas.MatchPrediction/Models/GenotypeMatchDetails.cs
@@ -12,7 +12,7 @@ public class GenotypeMatchDetails
         public decimal DonorGenotypeLikelihood { get; set; }
         public LociInfo<int?> MatchCounts { get; set; }
         public ISet<Locus> AvailableLoci { get; set; }
-        public int MatchCount => MatchCounts.Reduce((locus, value, accumulator) => accumulator + value ?? accumulator, 0);
+        public int MatchCount => MatchCounts.Reduce((_, value, accumulator) => accumulator + value ?? accumulator, 0);
         public int MismatchCount => (AvailableLoci.Count * 2) - MatchCount;
     }
 }