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refactor: #1294: Move match prediction debug models to debug client m…
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…odels namespace.
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zabeen committed May 2, 2024
1 parent f544488 commit 840107c
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Showing 41 changed files with 57 additions and 66 deletions.
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using System;

namespace Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet
namespace Atlas.Common.Public.Models.MatchPrediction
{
/// <summary>
/// This is the data used to determine which frequency set to use, for both Donors and Patients.
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using Atlas.Common.Public.Models.GeneticData;
using System.Collections.Generic;
using Newtonsoft.Json;

namespace Atlas.MatchPrediction.Models
namespace Atlas.Common.Public.Models.MatchPrediction
{
/// <summary>
/// Parameters controlling Match Prediction behaviour (in addition to <see cref="SubjectData"/>)
Expand Down Expand Up @@ -33,4 +32,4 @@ public MatchPredictionParameters(ISet<Locus> allowedLoci, string matchingAlgorit
MatchingAlgorithmHlaNomenclatureVersion = matchingAlgorithmHlaNomenclatureVersion;
}
}
}
}
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using Atlas.MatchPrediction.Models;
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.Functions.Models.Debug
namespace Atlas.Debug.Client.Models.MatchPrediction
{
public class GenotypeImputationRequest
{
public SubjectInfo SubjectInfo { get; set; }

/// <summary>
/// <inheritdoc cref="MatchPrediction.Models.MatchPredictionParameters"/>
/// <inheritdoc cref="Common.Public.Models.MatchPrediction.MatchPredictionParameters"/>
/// </summary>
public MatchPredictionParameters MatchPredictionParameters { get; set; }
}
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using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Models;
using Atlas.Client.Models.Search.Results.MatchPrediction;
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.Functions.Models.Debug
namespace Atlas.Debug.Client.Models.MatchPrediction
{
public class GenotypeImputationResponse
{
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using Atlas.MatchPrediction.Models;
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.Functions.Models.Debug
namespace Atlas.Debug.Client.Models.MatchPrediction
{
public class GenotypeMatcherRequest
{
/// <summary>
/// <inheritdoc cref="MatchPrediction.Models.MatchPredictionParameters"/>
/// <inheritdoc cref="Common.Public.Models.MatchPrediction.MatchPredictionParameters"/>
/// </summary>
public MatchPredictionParameters MatchPredictionParameters { get; set; }

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using System.Collections.Generic;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Models;
using Atlas.Client.Models.Search.Results.MatchPrediction;
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.Functions.Models.Debug
namespace Atlas.Debug.Client.Models.MatchPrediction
{
public class GenotypeMatcherResponse
{
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using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.Functions.Models.Debug
namespace Atlas.Debug.Client.Models.MatchPrediction
{
public class SubjectInfo
{
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2 changes: 1 addition & 1 deletion Atlas.Functions/Services/MatchPredictionInputBuilder.cs
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using Atlas.Common.ApplicationInsights.Timing;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Functions.Settings;
using Atlas.MatchPrediction.ExternalInterface;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability;
using EnumStringValues;
using Microsoft.Extensions.Options;
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@@ -1,9 +1,9 @@
using System.IO;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Utils.Http;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Functions.Models.Debug;
using Atlas.Debug.Client.Models.MatchPrediction;
using Atlas.MatchPrediction.Functions.Services.Debug;
using Atlas.MatchPrediction.Models;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
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using Microsoft.AspNetCore.Mvc;
using Microsoft.Azure.WebJobs;
using Microsoft.Azure.WebJobs.Extensions.Http;
using MoreLinq;
using Newtonsoft.Json;

namespace Atlas.MatchPrediction.Functions.Functions.Debug
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{
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()
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@@ -1,7 +1,7 @@
using System.IO;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Utils.Http;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchPredictionSteps.GenotypeLikelihood;
using Atlas.MatchPrediction.Services.GenotypeLikelihood;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
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Expand Up @@ -2,8 +2,8 @@
using System.Threading.Tasks;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.Common.Utils.Http;
using Atlas.Debug.Client.Models.MatchPrediction;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Functions.Models.Debug;
using Atlas.MatchPrediction.Functions.Services.Debug;
using Atlas.MatchPrediction.Models;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
Expand Down Expand Up @@ -69,7 +69,7 @@ public class MatchCalculationFunctions
subjectResult.IsUnrepresented,
subjectResult.GenotypeCount,
subjectResult.SumOfLikelihoods,
set,
set.ToClientHaplotypeFrequencySet(),
subjectInfo.HlaTyping.ToPhenotypeInfo().PrettyPrint());
}

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Expand Up @@ -3,6 +3,7 @@
using System.Linq;
using System.Threading.Tasks;
using Atlas.Common.AzureEventGrid;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.MatchPrediction.ExternalInterface;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Models;
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@@ -1,11 +1,10 @@
using System.Collections.Generic;
using System.Threading.Tasks;
using Atlas.Common.GeneticData;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.MatchPrediction.Config;
using Atlas.MatchPrediction.Data.Models;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Services.GenotypeLikelihood;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies.Import;
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Expand Up @@ -6,6 +6,7 @@
using Microsoft.Extensions.DependencyInjection;
using NUnit.Framework;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.HlaMetadataDictionary.Test.IntegrationTests.TestHelpers.FileBackedStorageStubs;

namespace Atlas.MatchPrediction.Test.Integration.IntegrationTests.MatchPrediction.IndividualSteps.HaplotypeFrequencySetSelection
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Expand Up @@ -3,11 +3,11 @@
using System.Threading.Tasks;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.HlaMetadataDictionary.Test.IntegrationTests.TestHelpers.FileBackedStorageStubs;
using Atlas.MatchPrediction.Config;
using Atlas.MatchPrediction.Data.Models;
using Atlas.MatchPrediction.Models;
using Atlas.MatchPrediction.Models.FileSchema;
using Atlas.MatchPrediction.Services.CompressedPhenotypeExpansion;
using Atlas.MatchPrediction.Test.Integration.Resources.Alleles;
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@@ -1,8 +1,8 @@
using System.Threading.Tasks;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.HlaMetadataDictionary.Test.IntegrationTests.TestHelpers.FileBackedStorageStubs;
using Atlas.MatchPrediction.Models;
using Atlas.MatchPrediction.Services.CompressedPhenotypeExpansion;
using Atlas.MatchPrediction.Test.Integration.Resources.Alleles;
using FluentAssertions;
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@@ -1,12 +1,12 @@
using System.Threading.Tasks;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.MatchPrediction.Services.CompressedPhenotypeExpansion;
using Atlas.MatchPrediction.Test.Integration.Resources.Alleles;
using FluentAssertions;
using NUnit.Framework;
using static Atlas.MatchPrediction.Test.Integration.Resources.Alleles.Alleles;
using Atlas.MatchPrediction.Models;

namespace Atlas.MatchPrediction.Test.Integration.IntegrationTests.MatchPrediction.IndividualSteps.PhenotypeExpansion
{
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using System.Collections.Generic;
using System.Threading.Tasks;
using Atlas.Common.GeneticData;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.MatchPrediction.Data.Models;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Test.Integration.Resources.Alleles;
using Atlas.MatchPrediction.Test.TestHelpers.Builders.MatchProbabilityInputs;
using FluentAssertions;
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@@ -1,14 +1,12 @@
using System.Collections.Generic;
using System.Threading.Tasks;
using Atlas.Common.GeneticData;
using Atlas.Common.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.Common.Utils.Extensions;
using Atlas.MatchPrediction.Data.Models;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability;
using Atlas.MatchPrediction.Test.Integration.Resources.Alleles;
using Atlas.MatchPrediction.Test.TestHelpers.Builders;
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@@ -1,10 +1,10 @@
using System.Collections.Generic;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.HlaMetadataDictionary.Test.IntegrationTests.TestHelpers.FileBackedStorageStubs;
using Atlas.MatchPrediction.Data.Models;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability;
using Atlas.MatchPrediction.Models.FileSchema;
using Atlas.MatchPrediction.Services.MatchProbability;
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@@ -1,10 +1,9 @@
using System.Reflection;
using System.Threading.Tasks;
using Atlas.Common.GeneticData;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies.Import;
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@@ -1,5 +1,5 @@
using System.Threading.Tasks;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.MatchPrediction.Test.Integration.TestHelpers;
using Atlas.MatchPrediction.Test.TestHelpers.Builders.MatchProbabilityInputs;
using NUnit.Framework;
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@@ -1,5 +1,5 @@
using System.Threading.Tasks;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.MatchPrediction.Test.Integration.TestHelpers;
using Atlas.MatchPrediction.Test.TestHelpers.Builders.MatchProbabilityInputs;
using NUnit.Framework;
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@@ -1,11 +1,10 @@
using System.Collections.Generic;
using System.Reflection;
using System.Threading.Tasks;
using Atlas.Common.GeneticData;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers;
using Atlas.Common.Test.SharedTestHelpers.Builders;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies.Import;
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@@ -1,7 +1,7 @@
using System.Collections.Generic;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.MatchPrediction.Data.Models;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Models.FileSchema;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies;
using Atlas.MatchPrediction.Services.HaplotypeFrequencies.Import;
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@@ -1,7 +1,6 @@
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.MatchPrediction.ExternalInterface.Models;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.MatchPrediction.Test.Validation.Data.Models;
using Atlas.MatchPrediction.Test.Validation.Data.Repositories;
using Atlas.MatchPrediction.Test.Validation.Models;
Expand All @@ -14,6 +13,7 @@
using System.Linq;
using System.Net.Http;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.MatchPrediction;
using MatchPredictionRequest = Atlas.MatchPrediction.Test.Validation.Data.Models.MatchPredictionRequest;

namespace Atlas.MatchPrediction.Test.Validation.Services.Exercise3
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Expand Up @@ -13,6 +13,7 @@
using System.Collections.Generic;
using System.Linq;
using System.Threading.Tasks;
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.Test.Services.MatchProbability
{
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using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.Common.Public.Models.MatchPrediction;
using LochNessBuilder;

namespace Atlas.MatchPrediction.Test.TestHelpers.Builders
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@@ -1,10 +1,9 @@
using System.Collections.Generic;
using System.Linq;
using Atlas.Common.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.Common.Test.SharedTestHelpers;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Builder = LochNessBuilder.Builder<Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability.DonorInput>;

namespace Atlas.MatchPrediction.Test.TestHelpers.Builders.MatchProbabilityInputs
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@@ -1,9 +1,7 @@
using Atlas.Common.GeneticData;
using Atlas.Common.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.Common.Public.Models.MatchPrediction;
using LochNessBuilder;
using Builder = LochNessBuilder.Builder<Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability.IdentifiedMatchProbabilityRequest>;

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using Atlas.Common.GeneticData;
using Atlas.Common.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo;
using Atlas.Common.Public.Models.GeneticData.PhenotypeInfo.TransferModels;
using Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet;
using Atlas.Common.Public.Models.MatchPrediction;
using Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability;
using LochNessBuilder;
using Builder = LochNessBuilder.Builder<Atlas.MatchPrediction.ExternalInterface.Models.MatchProbability.SingleDonorMatchProbabilityInput>;
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Expand Up @@ -9,7 +9,7 @@ public class HaplotypeFrequencySet
public string Name { get; set; }
public int PopulationId { get; set; }

internal Client.Models.Search.Results.MatchPrediction.HaplotypeFrequencySet ToClientHaplotypeFrequencySet()
public Client.Models.Search.Results.MatchPrediction.HaplotypeFrequencySet ToClientHaplotypeFrequencySet()
{
return new Client.Models.Search.Results.MatchPrediction.HaplotypeFrequencySet
{
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@@ -1,4 +1,6 @@
namespace Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet
using Atlas.Common.Public.Models.MatchPrediction;

namespace Atlas.MatchPrediction.ExternalInterface.Models.HaplotypeFrequencySet
{
public class HaplotypeFrequencySetInput
{
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