Merge pull request #3395 from Open-Systems-Pharmacology/3394-add-registration-for-ospsuitecoreicoreusersettings-in-pksimr

Fixes #3394 Add registration for OSPSuite.Core.ICoreUserSettings in P…

Author: rwmcintosh

src/PKSim.R/Bootstrap/ApplicationStartup.cs

@@ -70,7 +70,7 @@ private IContainer performInitialization()
       private void registerMinimalImplementations(IContainer container)
       {
          container.Register<ICoreWorkspace, IWorkspace, CLIWorkspace>(LifeStyle.Singleton);
-         container.Register<ICoreUserSettings, CLIUserSettings>(LifeStyle.Singleton);
+         container.Register<OSPSuite.Core.ICoreUserSettings, ICoreUserSettings, CLIUserSettings>(LifeStyle.Singleton);
          container.Register<IProgressUpdater, NoneProgressUpdater>();
          container.Register<IOntogenyTask, CLIIndividualOntogenyTask>();
       }

tests/PKSim.R.Tests/ContextForStaticIntegration.cs

@@ -0,0 +1,18 @@
+using System;
+using NUnit.Framework;
+using OSPSuite.BDDHelper;
+
+namespace PKSim.R;
+
+[IntegrationTests]
+[Category("R")]
+public abstract class ContextForStaticIntegration : StaticContextSpecification
+{
+   public override void GlobalContext()
+   {
+      base.GlobalContext();
+      Api.InitializeOnce();
+
+      Environment.CurrentDirectory = AppDomain.CurrentDomain.BaseDirectory;
+   }
+}

tests/PKSim.R.Tests/Data/Atazanavir-Model_1Sim.json

@@ -0,0 +1,98 @@
+{
+  "Version": 76,
+  "Individuals": [
+    {
+      "Name": "Acosta2007",
+      "Seed": 8908561,
+      "OriginData": {
+        "CalculationMethods": [
+          "SurfaceAreaPlsInt_VAR1",
+          "Body surface area - Mosteller"
+        ],
+        "Species": "Human",
+        "Population": "WhiteAmerican_NHANES_1997",
+        "Gender": "MALE",
+        "Age": {
+          "Value": 34.0,
+          "Unit": "year(s)"
+        },
+        "Weight": {
+          "Value": 78.0,
+          "Unit": "kg"
+        }
+      },
+      "Molecules": [
+        {
+          "Name": "CYP3A4",
+          "Type": "Enzyme",
+          "MembraneLocation": "Apical",
+          "TissueLocation": "Intracellular",
+          "IntracellularVascularEndoLocation": "Endosomal",
+          "Expression": [
+            {
+              "Name": "Brain",
+              "Value": 0.0041682898325
+            },
+            {
+              "Name": "Gonads",
+              "Value": 0.00078691079081
+            },
+            {
+              "Name": "Kidney",
+              "Value": 0.0053603428126
+            },
+            {
+              "Name": "Periportal",
+              "Value": 1.0
+            },
+            {
+              "Name": "Pericentral",
+              "Value": 1.0
+            },
+            {
+              "Name": "Lung",
+              "Value": 0.00042695753798
+            },
+            {
+              "Name": "SmallIntestine",
+              "Value": 0.0727697702
+            },
+            {
+              "Name": "Duodenum",
+              "Value": 0.0727697702
+            },
+            {
+              "Name": "UpperJejunum",
+              "Value": 0.0727697702
+            },
+            {
+              "Name": "LowerJejunum",
+              "Value": 0.0727697702
+            },
+            {
+              "Name": "UpperIleum",
+              "Value": 0.0727697702
+            },
+            {
+              "Name": "LowerIleum",
+              "Value": 0.0727697702
+            }
+          ],
+          "Ontogeny": {
+            "Name": "CYP3A4"
+          },
+          "Parameters": [
+            {
+              "Name": "t1/2 (liver)",
+              "Value": 22.0,
+              "Unit": "h",
+              "ValueOrigin": {
+                "Source": "Unknown"
+              }
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}

tests/PKSim.R.Tests/DomainHelperForSpecs.cs

@@ -0,0 +1,11 @@
+using System;
+using System.IO;
+
+namespace PKSim.R;
+
+internal static class DomainHelperForSpecs
+{
+   private static readonly string _pathToData = "..\\..\\..\\Data\\";
+
+   public static string DataFilePathFor(string fileNameWithExtension) => Path.Combine(AppDomain.CurrentDomain.BaseDirectory, _pathToData, fileNameWithExtension);
+}

tests/PKSim.R.Tests/PKSim.R.Tests.csproj

@@ -54,6 +54,7 @@
   </ItemGroup>
 
   <ItemGroup>
+    <Folder Include="Data\" />
     <Folder Include="Properties\" />
   </ItemGroup>
 

tests/PKSim.R.Tests/RunSnapshotSpecs.cs

@@ -0,0 +1,45 @@
+using System;
+using OSPSuite.BDDHelper;
+using OSPSuite.BDDHelper.Extensions;
+using OSPSuite.CLI.Core.RunOptions;
+using OSPSuite.CLI.Core.Services;
+using OSPSuite.Utility;
+using System.IO;
+
+namespace PKSim.R;
+
+internal class RunSnapshotSpecs : ContextForStaticIntegration
+{
+   private readonly string _inputFolder = @"C:\Input\";
+   private readonly string _outputFolder = @"C:\Output\";
+
+   protected override void Context()
+   {
+      base.Context();
+      var runOptions = new SnapshotRunOptions
+      {
+         InputFolder = _inputFolder,
+         OutputFolder = _outputFolder,
+         ExportMode = SnapshotExportMode.Project
+      };
+
+      DirectoryHelper.CreateDirectory(_inputFolder);
+      FileHelper.Copy(DomainHelperForSpecs.DataFilePathFor("Atazanavir-Model_1Sim.json"), Path.Join(_inputFolder, "Atazanavir-Model_1Sim.json"));
+
+      Api.RunSnapshot(runOptions);
+   }
+
+   [Observation]
+   public void the_output_folder_contains_one_pksim5_file()
+   {
+      Directory.Exists(_outputFolder).ShouldBeTrue();
+      File.Exists(Path.Join(_outputFolder, "Atazanavir-Model_1Sim.pksim5")).ShouldBeTrue();
+   }
+
+   public override void Cleanup()
+   {
+      base.Cleanup();
+      DirectoryHelper.DeleteDirectory(_outputFolder, true);
+      DirectoryHelper.DeleteDirectory(_inputFolder, true);
+   }
+}