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Fixes #2402 Load simulations from a MoBi snapshot (#2403)
* Fixes #2402 Load simulations from a MoBi snapshot * Unwrap async exceptions with GetAwaiter().GetResult() * Document case-sensitive name matching in LoadSimulationsFromSnapshot * Use unique temp folders for SnapshotTask integration spec
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‎src/MoBi.R/Api.cs‎

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@@ -46,6 +46,8 @@ public static void InitializeOnce(ApiConfig apiConfig)
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public static IPassiveTransportsTask GetPassiveTransportsTask() => resolveTask<IPassiveTransportsTask>();
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public static ISnapshotTask GetSnapshotTask() => resolveTask<ISnapshotTask>();
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private static T resolveTask<T>()
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{
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try

‎src/MoBi.R/Services/SnapshotTask.cs‎

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using System;
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using System.Linq;
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using OSPSuite.CLI.Core.RunOptions;
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using OSPSuite.CLI.Core.Services;
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using MoBiSimulation = MoBi.R.Domain.MoBiSimulation;
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using CoreSnapshotTask = MoBi.Core.Snapshots.Services.ISnapshotTask;
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namespace MoBi.R.Services
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{
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public interface ISnapshotTask
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{
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/// <summary>
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/// Loads the simulations stored in the snapshot file at <paramref name="snapshotFile" />. If
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/// <paramref name="simulationNames" /> is provided, only the simulations whose names match are returned.
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/// Matching is ordinal and case-sensitive, consistent with the rest of the OSP suite's name lookups.
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/// When no name is supplied, every simulation contained in the snapshot is returned (equivalent to opening the
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/// snapshot in MoBi).
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/// </summary>
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MoBiSimulation[] LoadSimulationsFromSnapshot(string snapshotFile, params string[] simulationNames);
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/// <summary>
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/// Runs the snapshot workflow for the given <paramref name="inputFolder" /> and <paramref name="outputFolder" />
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/// using sensible defaults for the remaining options. Optional <paramref name="folders" /> can be provided to
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/// process each folder pair instead of the single input/output pair.
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/// </summary>
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void RunSnapshot(string inputFolder, string outputFolder, bool runSimulations = true,
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SnapshotExportMode exportMode = SnapshotExportMode.Snapshot, params string[] folders);
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}
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public class SnapshotTask : ISnapshotTask
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{
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private readonly CoreSnapshotTask _snapshotTask;
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private readonly IBatchRunner<SnapshotRunOptions> _snapshotRunner;
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public SnapshotTask(CoreSnapshotTask snapshotTask, IBatchRunner<SnapshotRunOptions> snapshotRunner)
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{
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_snapshotTask = snapshotTask;
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_snapshotRunner = snapshotRunner;
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}
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public MoBiSimulation[] LoadSimulationsFromSnapshot(string snapshotFile, params string[] simulationNames)
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{
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var project = _snapshotTask.LoadProjectFromSnapshotFileAsync(snapshotFile).GetAwaiter().GetResult();
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if (project == null)
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return Array.Empty<MoBiSimulation>();
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var allSimulations = project.Simulations;
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var matched = simulationNames.Length == 0
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? allSimulations
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: allSimulations.Where(x => simulationNames.Contains(x.Name));
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return matched.Select(x => new MoBiSimulation(x)).ToArray();
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}
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public void RunSnapshot(string inputFolder, string outputFolder, bool runSimulations = true,
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SnapshotExportMode exportMode = SnapshotExportMode.Snapshot, params string[] folders)
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{
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var runOptions = new SnapshotRunOptions
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{
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InputFolder = inputFolder,
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OutputFolder = outputFolder,
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RunSimulations = runSimulations,
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ExportMode = exportMode,
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Folders = folders
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};
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_snapshotRunner.RunBatchAsync(runOptions).GetAwaiter().GetResult();
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}
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}
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}

‎src/MoBi.R/Services/StartableProcessFactory.cs‎

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using OSPSuite.Core.Services;
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namespace MoBi.R.Services
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{
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/// <summary>
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/// Minimal <see cref="IStartableProcessFactory" /> for the MoBi.R container. The real OSPSuite.Core registration
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/// relies on Castle Windsor's typed-factory feature, which the Autofac container used by MoBi.R does not synthesize.
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/// Providing an explicit implementation lets <c>PKSimStarter</c> (and therefore the snapshot mappers) resolve so
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/// snapshots that contain PK-Sim modules can be re-built in R workflows.
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/// </summary>
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public class StartableProcessFactory : IStartableProcessFactory
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{
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public StartableProcess CreateStartableProcess(string applicationPath, params string[] arguments) =>
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new StartableProcess(applicationPath, arguments);
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}
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}

‎tests/MoBi.R.Tests/Data/snapshot_no_pksim_modules.json‎

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‎tests/MoBi.R.Tests/MoBi.R.Tests.csproj‎

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<None Update="Data\simulation with two modules.pkml">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</None>
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<None Update="Data\snapshot_no_pksim_modules.json">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</None>
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<None Update="OSPSuite.Dimensions.xml">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</None>

‎tests/MoBi.R.Tests/Services/SnapshotTaskSpecs.cs‎

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using System;
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using System.IO;
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using System.Linq;
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using OSPSuite.BDDHelper;
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using OSPSuite.BDDHelper.Extensions;
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using OSPSuite.CLI.Core.Services;
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using OSPSuite.Utility;
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using static MoBi.R.Tests.HelperForSpecs;
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using MoBiSimulation = MoBi.R.Domain.MoBiSimulation;
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using ISnapshotTask = MoBi.R.Services.ISnapshotTask;
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namespace MoBi.R.Tests.Services
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{
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internal abstract class concern_for_SnapshotTask : ContextForIntegration<ISnapshotTask>
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{
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protected string _snapshotFile;
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public override void GlobalContext()
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{
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base.GlobalContext();
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sut = Api.GetSnapshotTask();
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}
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protected override void Context()
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{
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base.Context();
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_snapshotFile = DataTestFileFullPath("snapshot_no_pksim_modules.json");
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}
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}
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internal class When_loading_all_simulations_from_a_snapshot : concern_for_SnapshotTask
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{
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private MoBiSimulation[] _simulations;
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protected override void Because()
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{
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_simulations = sut.LoadSimulationsFromSnapshot(_snapshotFile);
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}
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[Observation]
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public void should_return_every_simulation_defined_in_the_snapshot()
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{
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_simulations.ShouldNotBeNull();
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_simulations.Length.ShouldBeGreaterThan(0);
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}
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}
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internal class When_loading_simulations_filtered_by_an_existing_simulation_name : concern_for_SnapshotTask
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{
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private MoBiSimulation[] _simulations;
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private string _existingSimulationName;
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protected override void Context()
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{
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base.Context();
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_existingSimulationName = sut.LoadSimulationsFromSnapshot(_snapshotFile).First().Name;
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}
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protected override void Because()
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{
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_simulations = sut.LoadSimulationsFromSnapshot(_snapshotFile, _existingSimulationName);
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}
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[Observation]
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public void should_return_only_simulations_whose_name_matches()
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{
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_simulations.Length.ShouldBeEqualTo(1);
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_simulations[0].Name.ShouldBeEqualTo(_existingSimulationName);
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}
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}
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internal class When_loading_simulations_filtered_by_a_name_that_does_not_exist : concern_for_SnapshotTask
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{
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private MoBiSimulation[] _simulations;
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protected override void Because()
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{
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_simulations = sut.LoadSimulationsFromSnapshot(_snapshotFile, "ThisSimulationDoesNotExist");
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}
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[Observation]
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public void should_return_an_empty_array()
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{
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_simulations.Length.ShouldBeEqualTo(0);
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}
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}
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internal class When_running_a_snapshot_export_using_the_convenient_method : concern_for_SnapshotTask
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{
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private readonly string _inputFolder = Path.Combine(Path.GetTempPath(), $"MoBi_SnapshotTask_Input_{Guid.NewGuid():N}");
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private readonly string _outputFolder = Path.Combine(Path.GetTempPath(), $"MoBi_SnapshotTask_Output_{Guid.NewGuid():N}");
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private readonly string _snapshotFileName = "snapshot_no_pksim_modules.json";
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protected override void Context()
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{
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base.Context();
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DirectoryHelper.CreateDirectory(_inputFolder);
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FileHelper.Copy(_snapshotFile, Path.Combine(_inputFolder, _snapshotFileName));
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}
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protected override void Because()
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{
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sut.RunSnapshot(_inputFolder, _outputFolder, exportMode: SnapshotExportMode.Project);
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}
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[Observation]
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public void should_write_the_mbp3_project_file_to_the_output_folder()
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{
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Directory.Exists(_outputFolder).ShouldBeTrue();
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File.Exists(Path.Combine(_outputFolder, "snapshot_no_pksim_modules.mbp3")).ShouldBeTrue();
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}
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public override void Cleanup()
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{
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base.Cleanup();
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DirectoryHelper.DeleteDirectory(_outputFolder, true);
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DirectoryHelper.DeleteDirectory(_inputFolder, true);
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}
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}
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}

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