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feature: #964: Report discrepant results from exercise 1 of wmda cons…
…ensus dataset.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| using CsvHelper; | ||
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| namespace Atlas.ManualTesting.Common | ||
| { | ||
| public interface IFileReader<T> | ||
| { | ||
| Task<IReadOnlyCollection<T>> ReadAllLines(string delimiter, string filePath); | ||
| IAsyncEnumerable<T> ReadAsync(string delimiter, string filePath); | ||
| } | ||
|
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| public class FileReader<T> : IFileReader<T> | ||
| { | ||
| public async Task<IReadOnlyCollection<T>> ReadAllLines(string delimiter, string filePath) | ||
| { | ||
| FileChecks(filePath); | ||
|
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| await using var stream = File.OpenRead(filePath); | ||
| using var reader = new StreamReader(stream); | ||
| using var csv = new CsvReader(reader); | ||
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| csv.Configuration.Delimiter = delimiter; | ||
| csv.Configuration.HeaderValidated = null; | ||
| csv.Configuration.MissingFieldFound = null; | ||
| csv.Configuration.TypeConverterOptionsCache.GetOptions<string>().NullValues.Add(""); | ||
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| return csv.GetRecords<T>().ToList(); | ||
| } | ||
|
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| public async IAsyncEnumerable<T> ReadAsync(string delimiter, string filePath) | ||
| { | ||
| FileChecks(filePath); | ||
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| await using var stream = File.OpenRead(filePath); | ||
| using var reader = new StreamReader(stream); | ||
| using var csv = new CsvReader(reader); | ||
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| csv.Configuration.Delimiter = delimiter; | ||
| csv.Configuration.HeaderValidated = null; | ||
| csv.Configuration.MissingFieldFound = null; | ||
| csv.Configuration.TypeConverterOptionsCache.GetOptions<string>().NullValues.Add(""); | ||
|
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| await csv.ReadAsync(); | ||
| csv.ReadHeader(); | ||
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| while (await csv.ReadAsync()) | ||
| { | ||
| yield return csv.GetRecord<T>(); | ||
| } | ||
| } | ||
|
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| private static void FileChecks(string filePath) | ||
| { | ||
| if (string.IsNullOrEmpty(filePath)) | ||
| { | ||
| throw new ArgumentNullException(nameof(filePath)); | ||
| } | ||
|
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| if (!File.Exists(filePath)) | ||
| { | ||
| throw new ArgumentException($"File not found at {filePath}."); | ||
| } | ||
| } | ||
| } | ||
| } |
36 changes: 0 additions & 36 deletions
36
Atlas.ManualTesting.Common/SubjectImport/SubjectInfoReader.cs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| namespace Atlas.ManualTesting.Models | ||
| { | ||
| public class ReportDiscrepanciesRequest | ||
| { | ||
| /// <summary> | ||
| /// Path to file with consensus results | ||
| /// </summary> | ||
| public string ConsensusFilePath { get; set; } | ||
|
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| /// <summary> | ||
| /// Path to file with Atlas results that should be compared to the <see cref="ConsensusFilePath"/> | ||
| /// </summary> | ||
| public string ResultsFilePath { get; set; } | ||
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| /// <summary> | ||
| /// Path to file containing patient HLA | ||
| /// </summary> | ||
| public string PatientFilePath { get; set; } | ||
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| /// <summary> | ||
| /// Path to file containing donor HLA | ||
| /// </summary> | ||
| public string DonorFilePath { get; set; } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| using System; | ||
| using System.Collections.Generic; | ||
| using System.Diagnostics; | ||
| using System.Net.Http; | ||
| using System.Threading.Tasks; | ||
| using Atlas.Common.Public.Models.GeneticData; | ||
| using Atlas.HlaMetadataDictionary.ExternalInterface.Models; | ||
| using Atlas.ManualTesting.Settings; | ||
| using Microsoft.Extensions.Options; | ||
| using Newtonsoft.Json; | ||
| using Polly; | ||
|
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| namespace Atlas.ManualTesting.Services | ||
| { | ||
| /// <summary> | ||
| /// Copied <see cref="Atlas.MatchingAlgorithm.Functions.Models.Debug.HlaConversionRequest"/>, | ||
| /// instead of moving the model to the MatchingAlgorithm.Client.Models project, | ||
| /// to avoid breaking client/interface changes that would come from moving <see cref="Atlas.HlaMetadataDictionary.ExternalInterface.Models.TargetHlaCategory"/>. | ||
| /// </summary> | ||
| public class ConvertHlaRequest | ||
| { | ||
| public Locus Locus { get; set; } | ||
| public string HlaName { get; set; } | ||
| public TargetHlaCategory TargetHlaCategory { get; set; } | ||
|
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| public override string ToString() | ||
| { | ||
| return $"convert {Locus},{HlaName} to {TargetHlaCategory}"; | ||
| } | ||
| } | ||
|
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| public interface IConvertHlaRequester | ||
| { | ||
| Task<IEnumerable<string>> ConvertHla(ConvertHlaRequest request); | ||
| } | ||
|
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| internal class ConvertHlaRequester : IConvertHlaRequester | ||
| { | ||
| private const string FailedRequestPrefix = "Failed to"; | ||
| private static readonly HttpClient HttpRequestClient = new(); | ||
| private readonly HlaMetadataDictionarySettings hlaMetadataDictionarySettings; | ||
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| public ConvertHlaRequester(IOptions<HlaMetadataDictionarySettings> settings) | ||
| { | ||
| hlaMetadataDictionarySettings = settings.Value; | ||
| } | ||
|
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| public async Task<IEnumerable<string>> ConvertHla(ConvertHlaRequest request) | ||
| { | ||
| if (request?.HlaName is null) | ||
| { | ||
| throw new ArgumentException("ConvertHla request is missing required data."); | ||
| } | ||
|
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| return await ExecuteHlaConversionRequest(request); | ||
| } | ||
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| private async Task<IEnumerable<string>> ExecuteHlaConversionRequest(ConvertHlaRequest request) | ||
| { | ||
| var retryPolicy = Policy.Handle<Exception>().RetryAsync(10); | ||
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| var requestResponse = await retryPolicy.ExecuteAndCaptureAsync(async () => await SendHlaConversionRequest(request)); | ||
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| return requestResponse.Outcome == OutcomeType.Successful | ||
| ? requestResponse.Result | ||
| : new[] { $"{FailedRequestPrefix} {request}" }; | ||
| } | ||
|
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| private async Task<IReadOnlyCollection<string>> SendHlaConversionRequest(ConvertHlaRequest request) | ||
| { | ||
| try | ||
| { | ||
| var response = await HttpRequestClient.PostAsync( | ||
| hlaMetadataDictionarySettings.ConvertHlaRequestUrl, new StringContent(JsonConvert.SerializeObject(request))); | ||
| response.EnsureSuccessStatusCode(); | ||
| var hlaConversionResult = JsonConvert.DeserializeObject<List<string>>(await response.Content.ReadAsStringAsync()); | ||
|
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| Debug.WriteLine($"Result received: {request}"); | ||
|
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| return hlaConversionResult; | ||
| } | ||
| catch (Exception ex) | ||
| { | ||
| Debug.WriteLine($"{FailedRequestPrefix} {request}. Details: {ex.Message}. Re-attempting until success or re-attempt count reached."); | ||
| throw; | ||
| } | ||
| } | ||
| } | ||
| } |
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