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chore: #1294: Process all sets imported found in a directory.
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38
....MatchPrediction.Test.Validation.Data/Repositories/Homework/HomeworkDeletionRepository.cs
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|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| using Dapper; | ||
| using Microsoft.Data.SqlClient; | ||
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| namespace Atlas.MatchPrediction.Test.Validation.Data.Repositories.Homework | ||
| { | ||
| public interface IHomeworkDeletionRepository | ||
| { | ||
| Task DeleteAll(); | ||
| } | ||
|
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| public class HomeworkDeletionRepository : IHomeworkDeletionRepository | ||
| { | ||
| private readonly string connectionString; | ||
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| public HomeworkDeletionRepository(string connectionString) | ||
| { | ||
| this.connectionString = connectionString; | ||
| } | ||
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| /// <inheritdoc /> | ||
| public async Task DeleteAll() | ||
| { | ||
| const string deleteAllPairs = "DELETE FROM PatientDonorPairs"; | ||
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| await using (var connection = new SqlConnection(connectionString)) | ||
| { | ||
| await connection.ExecuteAsync(deleteAllPairs); | ||
| } | ||
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| const string deleteAllSets = "DELETE FROM HomeworkSets"; | ||
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| await using (var connection = new SqlConnection(connectionString)) | ||
| { | ||
| await connection.ExecuteAsync(deleteAllSets); | ||
| } | ||
| } | ||
| } | ||
| } |
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89 changes: 89 additions & 0 deletions
89
Atlas.MatchPrediction.Test.Validation/Services/Exercise4/Homework/HomeworkCreator.cs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| using System.Collections.Generic; | ||
| 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; | ||
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| namespace Atlas.MatchPrediction.Test.Validation.Services.Exercise4.Homework | ||
| { | ||
| public interface IHomeworkCreator | ||
| { | ||
| /// <summary> | ||
| /// Creates new homework sets from the input files defined in the request. | ||
| /// </summary> | ||
| /// <returns>Homework Set Ids</returns> | ||
| Task<IEnumerable<int>> CreateHomeworkSets(HomeworkRequest request); | ||
| } | ||
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| internal class HomeworkCreator : IHomeworkCreator | ||
| { | ||
| private const string FileDelimiter = ","; | ||
| private readonly IHomeworkSetRepository setRepository; | ||
| private readonly IFileReader<SubjectIdPair> fileReader; | ||
| private readonly IPatientDonorPairRepository pdpRepository; | ||
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| public HomeworkCreator( | ||
| IHomeworkSetRepository setRepository, | ||
| IFileReader<SubjectIdPair> fileReader, | ||
| IPatientDonorPairRepository pdpRepository) | ||
| { | ||
| this.setRepository = setRepository; | ||
| this.fileReader = fileReader; | ||
| this.pdpRepository = pdpRepository; | ||
| } | ||
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| /// <inheritdoc /> | ||
| public async Task<IEnumerable<int>> CreateHomeworkSets(HomeworkRequest request) | ||
| { | ||
| var setIds = new List<int?>(); | ||
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| var fileNames = GetCsvFileNames(request.InputPath); | ||
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| foreach (var file in fileNames) | ||
| { | ||
| setIds.Add(await ImportPatientDonorPairs(request, file)); | ||
| } | ||
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| return setIds.Where(id => id.HasValue).Select(id => id.Value); | ||
| } | ||
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| private static IEnumerable<string> GetCsvFileNames(string path) | ||
| { | ||
| return Directory.GetFiles(path) | ||
| .Where(file => Path.GetExtension(file) == ".csv") | ||
| .Select(Path.GetFileName); | ||
| } | ||
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| private async Task<int?> ImportPatientDonorPairs(HomeworkRequest request, string setFileName) | ||
| { | ||
| var subjectIdPairs = await fileReader.ReadAllLines( | ||
| FileDelimiter, | ||
| Path.Combine(request.InputPath, setFileName), | ||
| hasHeaderRecord: false); | ||
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| if (subjectIdPairs.IsNullOrEmpty()) | ||
| { | ||
| System.Diagnostics.Debug.WriteLine($"No patient-donor pairs found in file {setFileName}."); | ||
| return null; | ||
| } | ||
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| var setId = await setRepository.Add(setFileName, request.ResultsPath, request.MatchLoci.MatchLociToString()); | ||
| await pdpRepository.BulkInsert(subjectIdPairs.Select(ids => MapToDatabaseModel(ids, setId)).ToList()); | ||
| return setId; | ||
| } | ||
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| private static PatientDonorPair MapToDatabaseModel(SubjectIdPair ids, int homeworkSetId) | ||
| { | ||
| return new PatientDonorPair | ||
| { | ||
| PatientId = ids.PatientId, | ||
| DonorId = ids.DonorId, | ||
| HomeworkSet_Id = homeworkSetId | ||
| }; | ||
| } | ||
| } | ||
| } |
65 changes: 65 additions & 0 deletions
65
Atlas.MatchPrediction.Test.Validation/Services/Exercise4/Homework/HomeworkProcessor.cs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| using System; | ||
| using System.Collections.Generic; | ||
| using System.Linq; | ||
| using System.Threading.Tasks; | ||
| using Atlas.Common.Utils.Extensions; | ||
| using Atlas.MatchPrediction.Test.Validation.Data.Repositories.Homework; | ||
| using Atlas.MatchPrediction.Test.Validation.Models; | ||
|
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| namespace Atlas.MatchPrediction.Test.Validation.Services.Exercise4.Homework | ||
| { | ||
| public interface IHomeworkProcessor | ||
| { | ||
| Task StartOrContinueHomeworkSets(IEnumerable<int> homeworkSetIds); | ||
| } | ||
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| internal class HomeworkProcessor : IHomeworkProcessor | ||
| { | ||
| private readonly IHomeworkSetRepository setRepository; | ||
| private readonly IPatientDonorPairRepository pdpRepository; | ||
| private readonly IPatientDonorPairProcessor pdpProcessor; | ||
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| public HomeworkProcessor( | ||
| IHomeworkSetRepository setRepository, | ||
| IPatientDonorPairRepository pdpRepository, | ||
| IPatientDonorPairProcessor pdpProcessor) | ||
| { | ||
| this.setRepository = setRepository; | ||
| this.pdpRepository = pdpRepository; | ||
| this.pdpProcessor = pdpProcessor; | ||
| } | ||
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| public async Task StartOrContinueHomeworkSets(IEnumerable<int> homeworkSetIds) | ||
| { | ||
| foreach (var homeworkSetId in homeworkSetIds) | ||
| { | ||
| await ProcessHomeworkSet(homeworkSetId); | ||
| } | ||
| } | ||
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| private async Task ProcessHomeworkSet(int homeworkSetId) | ||
| { | ||
| var set = await setRepository.Get(homeworkSetId); | ||
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| if (set == null) | ||
| { | ||
| throw new ArgumentException($"No homework set found with id {homeworkSetId}."); | ||
| } | ||
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| var pdps = (await pdpRepository.GetUnprocessedPairs(homeworkSetId)).ToList(); | ||
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| if (pdps.IsNullOrEmpty()) | ||
| { | ||
| System.Diagnostics.Debug.WriteLine($"No unprocessed patient-donor pairs found for homework set {homeworkSetId}."); | ||
| return; | ||
| } | ||
|
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| var matchLoci = set.MatchLoci.ToLociInfo(); | ||
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| foreach (var pdp in pdps) | ||
| { | ||
| await pdpProcessor.Process(pdp, matchLoci); | ||
| } | ||
| } | ||
| } | ||
| } |
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