chore: #1294: Import pdps directly from file.

Anthony-Nolan · Apr 27, 2024 · 89cec57 · 89cec57
1 parent fb6dc94
commit 89cec57
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Showing 5 changed files with 42 additions and 20 deletions.
diff --git a/Atlas.ManualTesting.Common/Services/FileReader.cs b/Atlas.ManualTesting.Common/Services/FileReader.cs
@@ -4,13 +4,16 @@ namespace Atlas.ManualTesting.Common.Services
 {
     public interface IFileReader<T>
     {
-        Task<IReadOnlyCollection<T>> ReadAllLines(string delimiter, string filePath);
+        Task<IReadOnlyCollection<T>> ReadAllLines(string delimiter, string filePath, bool hasHeaderRecord = true);
         IAsyncEnumerable<T> ReadAsync(string delimiter, string filePath);
     }
 
     public class FileReader<T> : IFileReader<T>
     {
-        public async Task<IReadOnlyCollection<T>> ReadAllLines(string delimiter, string filePath)
+        public async Task<IReadOnlyCollection<T>> ReadAllLines(
+            string delimiter,
+            string filePath,
+            bool hasHeaderRecord = true)
         {
             FileChecks(filePath);
 
@@ -19,6 +22,7 @@ public async Task<IReadOnlyCollection<T>> ReadAllLines(string delimiter, string
             using var csv = new CsvReader(reader);
 
             csv.Configuration.Delimiter = delimiter;
+            csv.Configuration.HasHeaderRecord = hasHeaderRecord;
             csv.Configuration.HeaderValidated = null;
             csv.Configuration.MissingFieldFound = null;
             csv.Configuration.TypeConverterOptionsCache.GetOptions<string>().NullValues.Add("");

diff --git a/Atlas.MatchPrediction.Test.Validation/DependencyInjection/ServiceConfiguration.cs b/Atlas.MatchPrediction.Test.Validation/DependencyInjection/ServiceConfiguration.cs
@@ -105,7 +105,7 @@ private static void RegisterDatabaseServices(this IServiceCollection services, F
             Func<IServiceProvider, ValidationSearchSettings> fetchValidationSearchSettings)
         {
             services.AddScoped<ISubjectInfoImporter, SubjectInfoImporter>();
-            services.AddScoped<IFileReader<ImportedSubject>, FileReader<ImportedSubject>>();
+            services.AddScoped(typeof(IFileReader<>), typeof(FileReader<>));
             services.AddScoped<ITestDonorExporter, TestDonorExporter>();
             services.AddScoped<ISearchRequester, SearchRequester>();
 

diff --git a/Atlas.MatchPrediction.Test.Validation/Models/HomeworkRequest.cs b/Atlas.MatchPrediction.Test.Validation/Models/HomeworkRequest.cs
@@ -1,14 +1,14 @@
 using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
-using System.Collections.Generic;
 
 namespace Atlas.MatchPrediction.Test.Validation.Models
 {
     public class HomeworkRequest
     {
         /// <summary>
-        /// Each string should have format: "PatientId,DonorId"
+        /// Path where homework set file should be read from.
+        /// Make sure to escape the backslashes in the path.
         /// </summary>
-        public IEnumerable<string> PatientDonorPairs { get; set; }
+        public string InputPath { get; set; }
 
         /// <summary>
         /// Path where results should be written to.
@@ -17,9 +17,9 @@ public class HomeworkRequest
         public string ResultsPath { get; set; }
 
         /// <summary>
-        /// Used to identify the result set.
+        /// Include the file extension, e.g., "A.csv".
         /// </summary>
-        public string HomeworkSetName { get; set; }
+        public string SetFileName { get; set; }
 
         /// <summary>
         /// Loci set to `true` will be included in the analysis.

diff --git a/Atlas.MatchPrediction.Test.Validation/Models/SubjectIdPair.cs b/Atlas.MatchPrediction.Test.Validation/Models/SubjectIdPair.cs
@@ -0,0 +1,8 @@
+namespace Atlas.MatchPrediction.Test.Validation.Models
+{
+    internal class SubjectIdPair
+    {
+        public string PatientId { get; set; }
+        public string DonorId { get; set; }
+    }
+}
diff --git a/...s.MatchPrediction.Test.Validation/Services/Exercise4/Homework/HomeworkRequestProcessor.cs b/...s.MatchPrediction.Test.Validation/Services/Exercise4/Homework/HomeworkRequestProcessor.cs
@@ -1,7 +1,9 @@
 using System;
+using System.IO;
 using System.Linq;
 using System.Threading.Tasks;
 using Atlas.Common.Utils.Extensions;
+using Atlas.ManualTesting.Common.Services;
 using Atlas.MatchPrediction.Test.Validation.Data.Models.Homework;
 using Atlas.MatchPrediction.Test.Validation.Data.Repositories.Homework;
 using Atlas.MatchPrediction.Test.Validation.Models;
@@ -18,25 +20,40 @@ public interface IHomeworkRequestProcessor
 
     internal class HomeworkRequestProcessor : IHomeworkRequestProcessor
     {
+        private const string FileDelimiter = ",";
         private readonly IHomeworkSetRepository setRepository;
+        private readonly IFileReader<SubjectIdPair> fileReader;
         private readonly IPatientDonorPairRepository pdpRepository;
         private readonly IPatientDonorPairProcessor pdpProcessor;
 
         public HomeworkRequestProcessor(
             IHomeworkSetRepository setRepository,
+            IFileReader<SubjectIdPair> fileReader,
             IPatientDonorPairRepository pdpRepository, 
             IPatientDonorPairProcessor pdpProcessor)
         {
             this.setRepository = setRepository;
+            this.fileReader = fileReader;
             this.pdpRepository = pdpRepository;
             this.pdpProcessor = pdpProcessor;
         }
 
         /// <inheritdoc />
         public async Task<int> StoreHomeworkRequest(HomeworkRequest request)
         {
-            var setId = await setRepository.Add(request.HomeworkSetName, request.ResultsPath, request.MatchLoci.MatchLociToString());
-            await pdpRepository.BulkInsert(request.PatientDonorPairs.Select(pdp => MapToDatabaseModel(pdp, setId)).ToList());
+            var subjectIdPairs = await fileReader.ReadAllLines(
+                FileDelimiter,
+                Path.Combine(request.InputPath, request.SetFileName),
+                hasHeaderRecord: false);
+
+            if (subjectIdPairs.IsNullOrEmpty())
+            {
+                throw new ArgumentException($"No patient-donor pairs found in file {request.SetFileName}.");
+            }
+
+            var setId = await setRepository.Add(request.SetFileName, request.ResultsPath, request.MatchLoci.MatchLociToString());
+
+            await pdpRepository.BulkInsert(subjectIdPairs.Select(ids => MapToDatabaseModel(ids, setId)).ToList());
             return setId;
         }
 
@@ -65,19 +82,12 @@ public async Task StartOrContinueHomeworkRequest(int homeworkSetId)
             }
         }
 
-        private static PatientDonorPair MapToDatabaseModel(string patientDonorPair, int homeworkSetId)
+        private static PatientDonorPair MapToDatabaseModel(SubjectIdPair ids, int homeworkSetId)
         {
-            var ids = patientDonorPair.Split(',');
-
-            if (ids.Length != 2)
-            {
-                throw new ArgumentException($"{nameof(patientDonorPair)} must contain exactly two ids separated by a comma; instead found {patientDonorPair}.");
-            }
-
             return new PatientDonorPair
             {
-                PatientId = ids[0],
-                DonorId = ids[1],
+                PatientId = ids.PatientId,
+                DonorId = ids.DonorId,
                 HomeworkSet_Id = homeworkSetId
             };
         }