chore: #1294: First check if db has existing imputaion results for su…

…bject.
Anthony-Nolan · May 2, 2024 · dcef5df · dcef5df
1 parent 7d97d33
commit dcef5df
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Showing 4 changed files with 46 additions and 6 deletions.
diff --git a/...MatchPrediction.Test.Validation.Data/Repositories/Homework/ImputationSummaryRepository.cs b/...MatchPrediction.Test.Validation.Data/Repositories/Homework/ImputationSummaryRepository.cs
@@ -8,6 +8,7 @@ namespace Atlas.MatchPrediction.Test.Validation.Data.Repositories.Homework
     public interface IImputationSummaryRepository
     {
         Task<int> Add(ImputationSummary imputationSummary);
+        Task<int?> Get(string externalSubjectId);
     }
 
     public class ImputationSummaryRepository : IImputationSummaryRepository
@@ -48,5 +49,19 @@ await using (var connection = new SqlConnection(connectionString))
                 })).Single();
             }
         }
+
+        /// <inheritdoc />
+        public async Task<int?> Get(string externalSubjectId)
+        {
+            const string sql = $@"
+                SELECT Id
+                FROM {nameof(MatchPredictionValidationContext.ImputationSummaries)}
+                WHERE ExternalSubjectId = @{nameof(externalSubjectId)}";
+
+            await using (var connection = new SqlConnection(connectionString))
+            {
+                return await connection.QuerySingleOrDefaultAsync<int?>(sql, new { externalSubjectId });
+            }
+        }
     }
 }
diff --git a/...s.MatchPrediction.Test.Validation.Data/Repositories/Homework/SubjectGenotypeRepository.cs b/...s.MatchPrediction.Test.Validation.Data/Repositories/Homework/SubjectGenotypeRepository.cs
@@ -1,11 +1,14 @@
 using Atlas.Common.Sql.BulkInsert;
 using Atlas.MatchPrediction.Test.Validation.Data.Context;
 using Atlas.MatchPrediction.Test.Validation.Data.Models.Homework;
+using Dapper;
+using Microsoft.Data.SqlClient;
 
 namespace Atlas.MatchPrediction.Test.Validation.Data.Repositories.Homework
 {
     public interface ISubjectGenotypeRepository : IBulkInsertRepository<SubjectGenotype>
     {
+        Task<IEnumerable<SubjectGenotype>> Get(int imputationSummaryId);
     }
 
     public class SubjectGenotypeRepository : BulkInsertRepository<SubjectGenotype>, ISubjectGenotypeRepository
@@ -16,5 +19,19 @@ public class SubjectGenotypeRepository : BulkInsertRepository<SubjectGenotype>,
         public SubjectGenotypeRepository(string connectionString) : base(connectionString, TableName)
         {
         }
+
+        /// <inheritdoc />
+        public async Task<IEnumerable<SubjectGenotype>> Get(int imputationSummaryId)
+        {
+            const string sql = $@"
+                SELECT * 
+                FROM {TableName} 
+                WHERE {nameof(SubjectGenotype.ImputationSummary_Id)} = @{nameof(imputationSummaryId)}";
+
+            await using (var connection = new SqlConnection(ConnectionString))
+            {
+                return await connection.QueryAsync<SubjectGenotype>(sql, new { imputationSummaryId });
+            }
+        }
     }
 }
diff --git a/....MatchPrediction.Test.Validation/Services/Exercise4/Homework/PatientDonorPairProcessor.cs b/....MatchPrediction.Test.Validation/Services/Exercise4/Homework/PatientDonorPairProcessor.cs
@@ -48,6 +48,10 @@ public async Task Process(PatientDonorPair pdp, string matchLoci, string hlaVers
                 Impute(pdp, donorResult, matchLoci, hlaVersion, false)
             // Then submit matching genotypes request
             );
+
+            // store matching genotypes after imputation as need the subject genotype ids
+
+            await UpdateRecord(pdp);
         }
 
         private async Task<SubjectGenotypeResult> CheckPatientHasMissingHla(PatientDonorPair pdp, LociInfo<bool> matchLoci)
@@ -85,8 +89,8 @@ async Task<SubjectGenotypeResult> GetResult()
             string hlaVersion,
             bool isPatient)
         {
-            // Only request imputation if subject has not been processed before
-            // This step should update the cache as well
+            // Only request imputation if subject has not been processed before.
+            // This step will update the cache as well.
             result.Genotypes ??= await genotypesProcessor.RequestAndSaveImputation(result.SubjectInfo, matchLoci, hlaVersion);
 
             if (isPatient)
@@ -97,8 +101,6 @@ async Task<SubjectGenotypeResult> GetResult()
             {
                 pdp.DonorImputationCompleted = true;
             }
-
-            await UpdateRecord(pdp);
         }
 
         private async Task UpdateRecord(PatientDonorPair pdp)

diff --git a/....MatchPrediction.Test.Validation/Services/Exercise4/Homework/SubjectGenotypesProcessor.cs b/....MatchPrediction.Test.Validation/Services/Exercise4/Homework/SubjectGenotypesProcessor.cs
@@ -41,6 +41,12 @@ internal class SubjectGenotypesProcessor : ISubjectGenotypesProcessor
             string hlaVersion)
         {
             var subjectId = subjectInfo.ExternalId;
+            var summaryId = await summaryRepo.Get(subjectId);
+
+            if (summaryId != null)
+            {
+                return await subjectGenotypeRepo.Get(summaryId.Value);
+            }
 
             var response = await imputationRequester.Request(new HomeworkImputationRequest
             {
@@ -57,8 +63,8 @@ internal class SubjectGenotypesProcessor : ISubjectGenotypesProcessor
                 return null;
             }
 
-            var summaryId = await summaryRepo.Add(BuildSummary(subjectId, response.Result!));
-            var genotypes = SplitIntoGenotypes(response.Result!.GenotypeLikelihoods, summaryId).ToList();
+            summaryId = await summaryRepo.Add(BuildSummary(subjectId, response.Result!));
+            var genotypes = SplitIntoGenotypes(response.Result!.GenotypeLikelihoods, summaryId.Value).ToList();
             await subjectGenotypeRepo.BulkInsert(genotypes);
             return genotypes;
         }