chore: #1294: Get and store genotypes.

Anthony-Nolan · May 1, 2024 · 46fde83 · 46fde83
1 parent 6ce207b
commit 46fde83
Show file tree

Hide file tree

Showing 29 changed files with 3,393 additions and 65 deletions.
diff --git a/Atlas.ManualTesting.Common/Services/HttpRequester.cs b/Atlas.ManualTesting.Common/Services/HttpRequester.cs
@@ -0,0 +1,56 @@
+using Newtonsoft.Json;
+using Polly;
+
+namespace Atlas.ManualTesting.Common.Services
+{
+    public class AtlasHttpResult<TResult>
+    {
+        public bool WasSuccess => Result != null;
+        public TResult? Result { get; set; }
+
+        public AtlasHttpResult(TResult? result)
+        {
+            Result = result;
+        }
+    }
+
+    public abstract class AtlasHttpRequester
+    {
+        private readonly HttpClient httpRequestClient;
+        private readonly string requestUrl;
+
+        protected AtlasHttpRequester(HttpClient httpRequestClient, string requestUrl)
+        {
+            this.httpRequestClient = httpRequestClient;
+            this.requestUrl = requestUrl;
+        }
+
+        protected async Task<AtlasHttpResult<TResult>> PostRequest<TRequest, TResult>(TRequest request)
+        {
+            var retryPolicy = Policy.Handle<Exception>().RetryAsync(10);
+
+            var requestResponse = await retryPolicy.ExecuteAndCaptureAsync(
+                async () => await SendRequest<TRequest, TResult>(request));
+
+            return new AtlasHttpResult<TResult>(requestResponse.Result);
+        }
+
+        private async Task<TResult?> SendRequest<TRequest, TResult>(TRequest request)
+        {
+            try
+            {
+                var response = await httpRequestClient.PostAsync(
+                    requestUrl, new StringContent(JsonConvert.SerializeObject(request)));
+                response.EnsureSuccessStatusCode();
+
+                return JsonConvert.DeserializeObject<TResult>(await response.Content.ReadAsStringAsync());
+            }
+            catch (Exception ex)
+            {
+                System.Diagnostics.Debug.WriteLine($"Failed to send request {request}. Details: {ex.Message} " +
+                                "Re-attempting until success or re-attempt count reached.");
+                throw;
+            }
+        }
+    }
+}
diff --git a/Atlas.MatchPrediction.Functions/Functions/Debug/GenotypeImputationFunctions.cs b/Atlas.MatchPrediction.Functions/Functions/Debug/GenotypeImputationFunctions.cs
@@ -51,7 +51,7 @@ public class GenotypeImputationFunctions
             {
                 HlaTyping = input.SubjectInfo.HlaTyping.ToPhenotypeInfo().PrettyPrint(),
                 MatchPredictionParameters = input.MatchPredictionParameters,
-                HaplotypeFrequencySet = frequencySet,
+                HaplotypeFrequencySet = frequencySet.ToClientHaplotypeFrequencySet(),
                 GenotypeCount = imputedGenotypes.GenotypeLikelihoods.Count,
                 SumOfLikelihoods = imputedGenotypes.SumOfLikelihoods,
                 GenotypeLikelihoods = imputedGenotypes.GenotypeLikelihoods.ToSingleDelimitedString()

diff --git a/Atlas.MatchPrediction.Functions/Functions/Debug/MatchCalculationFunctions.cs b/Atlas.MatchPrediction.Functions/Functions/Debug/MatchCalculationFunctions.cs
@@ -69,7 +69,7 @@ public class MatchCalculationFunctions
                 subjectResult.IsUnrepresented,
                 subjectResult.GenotypeCount,
                 subjectResult.SumOfLikelihoods,
-                set, 
+                set.ToClientHaplotypeFrequencySet(), 
                 subjectInfo.HlaTyping.ToPhenotypeInfo().PrettyPrint());
         }
     }

diff --git a/Atlas.MatchPrediction.Test.Validation.Data/Context/MatchPredictionValidationContext.cs b/Atlas.MatchPrediction.Test.Validation.Data/Context/MatchPredictionValidationContext.cs
@@ -29,6 +29,8 @@ protected override void OnModelCreating(ModelBuilder modelBuilder)
 
             modelBuilder.Entity<HomeworkSet>().SetUpModel();
             modelBuilder.Entity<PatientDonorPair>().SetUpModel();
+            modelBuilder.Entity<ImputationSummary>().SetUpModel();
+            modelBuilder.Entity<SubjectGenotype>().SetUpModel();
 
             base.OnModelCreating(modelBuilder);
         }
@@ -47,5 +49,7 @@ protected override void OnModelCreating(ModelBuilder modelBuilder)
 
         public DbSet<HomeworkSet> HomeworkSets { get; set; }
         public DbSet<PatientDonorPair> PatientDonorPairs { get; set; }
+        public DbSet<ImputationSummary> ImputationSummaries { get; set; }
+        public DbSet<SubjectGenotype> SubjectGenotypes { get; set; }
     }
 }