Add initialization service

#149

H.Core.Test/Services/InitializationServiceTest.cs

@@ -6,7 +6,13 @@
 using System.Collections.Generic;
 using H.Core.Enumerations;
 using H.Core.Models;
+using H.Core.Models.Animals;
+using H.Core.Providers.Animals;
 using H.Core.Services;
+using System.Linq;
+using H.Core.Models.Animals.Dairy;
+using Castle.DynamicProxy.Generators.Emitters.SimpleAST;
+using H.Core.Models.Animals.Beef;
 
 namespace H.Core.Test.Services
 {
@@ -56,7 +62,7 @@ public void TestCleanup()
         #endregion
 
         #region Tests
-        
+
         [TestMethod]
         public void ReInitializeFarmsTest()
         {
@@ -65,7 +71,184 @@ public void ReInitializeFarmsTest()
             _initializationService.ReInitializeFarms(_farms);
 
             Assert.AreEqual(_farm1.ClimateData.BarnTemperatureData.January, 2.767742149);
-        } 
+        }
+
+        [TestMethod]
+        public void InitializeDefaultEmissionFactorsUpdatesDefault()
+        {
+            var managementPeriod = new ManagementPeriod()
+            {
+                ManureDetails = new ManureDetails()
+                {
+                    StateType = ManureStateType.SolidStorage,
+                    MethaneConversionFactor = 4,
+                }
+            };
+
+            _initializationService.InitializeDefaultEmissionFactors(_farm1, new CowCalfComponent(), managementPeriod);
+
+            Assert.AreEqual(expected: 0.02, actual: managementPeriod.ManureDetails.MethaneConversionFactor);
+        }
+
+        [TestMethod]
+        public void InitializeManureMineralizationFractionsUpdatedDefaultValues()
+        {
+            var managementPeriod = new ManagementPeriod()
+            {
+                ManureDetails = new ManureDetails()
+                {
+                    FractionOfOrganicNitrogenNitrified = 10,
+                }
+            };
+
+            _initializationService.InitializeManureMineralizationFractions(managementPeriod, new FractionOfOrganicNitrogenMineralizedData() {FractionNitrified = 2});
+
+            Assert.AreEqual(expected: 2, actual: managementPeriod.ManureDetails.FractionOfOrganicNitrogenNitrified);
+        }
+
+        [TestMethod]
+        public void InitializeManureCompositionDataAssignsNewValueToManureDetails()
+        {
+            var managementPeriod = new ManagementPeriod()
+            {
+                ManureDetails = new ManureDetails()
+                {
+                    FractionOfPhosphorusInManure = 100,
+                }
+            };
+
+            var manureComposition = new DefaultManureCompositionData
+            {
+                PhosphorusFraction = 20
+            };
+
+            _initializationService.InitializeManureCompositionData(managementPeriod, manureComposition);
+
+            Assert.AreEqual(expected: 20, actual: managementPeriod.ManureDetails.FractionOfPhosphorusInManure);
+        }
+
+        [TestMethod]
+        public void ReinitializeAverageMilkProduction()
+        {
+            var dairycow = new AnimalGroup()
+            {
+                GroupType = AnimalType.DairyLactatingCow,
+                ManagementPeriods =
+                {
+                    new ManagementPeriod
+                    {
+                        Start = new DateTime(1990,  4, 25),
+                        MilkProduction = 200,
+
+                    }
+                },
+            };
+            var dairyComponent = new DairyComponent();
+            dairyComponent.Groups.Add(dairycow);
+            _farm1.Components.Add(dairyComponent);
+
+            _farm1.DairyComponents.Cast<DairyComponent>().First().Groups.Add(dairycow);
+            _farm1.DefaultSoilData.Province = Province.BritishColumbia;
+            _initializationService.InitializeMilkProduction(_farm1);
+            Assert.AreEqual(24.3, dairycow.ManagementPeriods.First().MilkProduction);
+
+        }
+        [TestMethod]
+        public void ReinitializeAverageMilkProductionYearNotFound()
+        {
+            var dairycow2 = new AnimalGroup()
+            {
+                GroupType = AnimalType.DairyLactatingCow,
+                ManagementPeriods =
+                {
+                    new ManagementPeriod
+                    {
+                        Start = new DateTime(1989,  4, 25),//invalid year
+                        MilkProduction = 200,
+
+                    }
+                },
+            };
+            var dairyComponent2 = new DairyComponent();
+            dairyComponent2.Groups.Add(dairycow2);
+            _farm2.Components.Add(dairyComponent2);
+            _farm2.DairyComponents.Cast<DairyComponent>().First().Groups.Add(dairycow2);
+            _farm2.DefaultSoilData.Province = Province.BritishColumbia;
+
+            Assert.ThrowsException<NullReferenceException>(() => _initializationService.InitializeMilkProduction(_farm2));
+        }
+        [TestMethod]
+        public void ReinitializeAverageMilkProductionIncorrectAnimalGroup()
+        {
+            var beef = new AnimalGroup()
+            {
+                GroupType = AnimalType.Beef,
+                ManagementPeriods =
+                {
+                    new ManagementPeriod
+                    {
+                        Start = new DateTime(1990,  4, 25),
+                        MilkProduction = 1000,
+
+                    }
+                },
+            };
+            var dairyComponent = new DairyComponent();
+            dairyComponent.Groups.Add(beef);
+            _farm1.Components.Add(dairyComponent);
+
+            _farm1.DairyComponents.Cast<DairyComponent>().First().Groups.Add(beef);
+            _farm1.DefaultSoilData.Province = Province.BritishColumbia;
+            _initializationService.InitializeMilkProduction(_farm1);
+            Assert.AreEqual(1000, beef.ManagementPeriods.First().MilkProduction);
+        }
+        [TestMethod]
+        public void ReinitializationAverageMilkProductionNullArgument()
+        {
+            Farm farm = new Farm();
+            try
+            {
+                _initializationService.InitializeMilkProduction(farm);
+            }
+            catch (Exception ex)
+            {
+                Assert.Fail(ex.Message);
+            }
+            var dairyComponent = new DairyComponent();
+            farm.Components.Add(dairyComponent);
+            try
+            {
+                _initializationService.InitializeMilkProduction(farm);
+            }
+            catch (Exception ex)
+            {
+                Assert.Fail(ex.Message);
+            }
+        }
+
+        [TestMethod]
+        public void InitializeBeddingMaterialSetsTotalCarbon()
+        {
+            var housingDetails = new HousingDetails();
+            housingDetails.TotalCarbonKilogramsDryMatterForBedding = 100;
+            housingDetails.BeddingMaterialType = BeddingMaterialType.Straw;
+
+            var managementPeriod = new ManagementPeriod();
+            managementPeriod.HousingDetails = housingDetails;
+            managementPeriod.AnimalType = AnimalType.BeefBackgrounderHeifer;
+
+            var animalGroup = new AnimalGroup();
+            animalGroup.ManagementPeriods.Add(managementPeriod);
+
+            var component = new CowCalfComponent();
+            component.Groups.Add(animalGroup);
+
+            _farm1.Components.Add(component);
+
+            _initializationService.ReinitializeBeddingMaterial(_farm1);
+
+            Assert.AreEqual(0.447, housingDetails.TotalCarbonKilogramsDryMatterForBedding);
+        }
 
         #endregion
     }

H.Core/Calculators/Nitrogen/N2OEmissionFactorCalculator.cs

@@ -405,6 +405,11 @@ public double CalculateTopographyEmissions(
 
             var result = 0.0;
 
+            /*
+             * Note the base Ef is not multiplied here by 100 as it is in the algorithm document since the FTopo value is a percentage in the lookup table and subsequently divided by 100. This negates the need to multiply
+             * by 100 as in the algorithm document.
+             */
+
             // For irrigated sites
             if (Math.Abs(growingSeasonPrecipitation - growingSeasonEvapotranspiration) < double.Epsilon)
             {

H.Core/Providers/Animals/Table_17_Beef_Dairy_Cattle_Feeding_Activity_Coefficient_Provider.cs

@@ -17,6 +17,7 @@ public Table_17_Beef_Dairy_Cattle_Feeding_Activity_Coefficient_Provider()
         {
             HTraceListener.AddTraceListener();
         }
+
         public IFeedingActivityCoeffientData GetByHousing(HousingType housingType)
         {
             switch (housingType)