Merge pull request #54 from bcgov/feature/VDYP-433

Refactor model objects so Site is a property of Species

vdyp-lib/pom.xml

@@ -3,9 +3,7 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
-	<groupId>ca.bc.gov.nrs.vdyp</groupId>
 	<artifactId>vdyp-lib</artifactId>
-	<version>0.0.1-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<name>Variable Density Yield Project - Library</name>

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/VdypStartApplication.java

@@ -69,7 +69,7 @@
 import ca.bc.gov.nrs.vdyp.model.VdypUtilizationHolder;
 import ca.bc.gov.nrs.vdyp.model.VolumeComputeMode;
 
-public abstract class VdypStartApplication<P extends BaseVdypPolygon<L, Optional<Float>, S, I>, L extends BaseVdypLayer<S, I> & InputLayer, S extends BaseVdypSpecies, I extends BaseVdypSite>
+public abstract class VdypStartApplication<P extends BaseVdypPolygon<L, Optional<Float>, S, I>, L extends BaseVdypLayer<S, I> & InputLayer, S extends BaseVdypSpecies<I>, I extends BaseVdypSite>
 		extends VdypApplication implements Closeable {
 
 	private static final Logger log = LoggerFactory.getLogger(VdypStartApplication.class);
@@ -170,8 +170,8 @@ protected static void doMain(VdypStartApplication<?, ?, ?, ?> app, final String.
 
 	public EstimationMethods estimationMethods;
 
-	static final Comparator<BaseVdypSpecies> PERCENT_GENUS_DESCENDING = Utils
-			.compareUsing(BaseVdypSpecies::getPercentGenus).reversed();
+	static final Comparator<BaseVdypSpecies<?>> PERCENT_GENUS_DESCENDING = Utils
+			.compareUsing(BaseVdypSpecies<?>::getPercentGenus).reversed();
 
 	/**
 	 * When finding primary species these genera should be combined
@@ -263,7 +263,7 @@ public void close() throws IOException {
 		closeVriWriter();
 	}
 
-	protected Coefficients getCoeForSpecies(BaseVdypSpecies species, ControlKey controlKey) {
+	protected Coefficients getCoeForSpecies(BaseVdypSpecies<?> species, ControlKey controlKey) {
 		var coeMap = Utils.<Map<String, Coefficients>>expectParsedControl(controlMap, controlKey, java.util.Map.class);
 		return coeMap.get(species.getGenus());
 	}
@@ -300,7 +300,7 @@ protected float getPercentTotal(L layer) throws StandProcessingException {
 		return percentTotal;
 	}
 
-	protected abstract S copySpecies(S toCopy, Consumer<BaseVdypSpecies.Builder<S>> config);
+	protected abstract S copySpecies(S toCopy, Consumer<BaseVdypSpecies.Builder<S, I, ?>> config);
 
 	/**
 	 * Returns the primary, and secondary if present species records as a one or two element list.
@@ -633,7 +633,8 @@ protected float estimatePrimaryBaseArea(
 
 	public S leadGenus(L fipLayer) {
 		return fipLayer.getSpecies().values().stream()
-				.sorted(Utils.compareUsing(BaseVdypSpecies::getFractionGenus).reversed()).findFirst().orElseThrow();
+				.sorted(Utils.compareUsing(BaseVdypSpecies<? extends BaseVdypSite>::getFractionGenus).reversed())
+				.findFirst().orElseThrow();
 	}
 
 	protected L getPrimaryLayer(P poly) throws StandProcessingException {
@@ -896,12 +897,17 @@ protected float estimatePrimaryQuadMeanDiameter(
 		return quadMeanDiameter;
 	}
 
-	protected Map<String, Float>
-			applyGroups(BaseVdypPolygon<?, ?, ?, ?> fipPolygon, Collection<VdypSpecies> vdypSpecies)
-					throws ProcessingException {
-		// Lookup volume group, Decay Group, and Breakage group for each species.
+	protected Map<String, Float> applyGroupsAndGetTargetPercentages(
+			BaseVdypPolygon<?, ?, ?, ?> fipPolygon, Collection<VdypSpecies> vdypSpecies
+	) throws ProcessingException {
 
-		Map<String, Float> targetPercentages = new HashMap<>(vdypSpecies.size());
+		applyGroups(fipPolygon, vdypSpecies);
+		return getTargetPercentages(vdypSpecies);
+	}
+
+	protected void applyGroups(BaseVdypPolygon<?, ?, ?, ?> fipPolygon, Collection<VdypSpecies> vdypSpecies)
+			throws ProcessingException {
+		// Lookup volume group, Decay Group, and Breakage group for each species.
 
 		BecDefinition bec = Utils.getBec(fipPolygon.getBiogeoclimaticZone(), controlMap);
 		var volumeGroupMap = getGroupMap(ControlKey.VOLUME_EQN_GROUPS);
@@ -919,6 +925,15 @@ protected float estimatePrimaryQuadMeanDiameter(
 			vSpec.setDecayGroup(decayGroup);
 			vSpec.setBreakageGroup(breakageGroup);
 
+		}
+
+	}
+
+	protected Map<String, Float> getTargetPercentages(Collection<VdypSpecies> vdypSpecies) {
+		Map<String, Float> targetPercentages = new HashMap<>(vdypSpecies.size());
+
+		for (var vSpec : vdypSpecies) {
+
 			targetPercentages.put(vSpec.getGenus(), vSpec.getPercentGenus());
 		}
 
@@ -1116,6 +1131,7 @@ private float meanVolumeSmall(VdypSpecies spec, float quadMeanDiameterSpecSmall,
 		);
 	}
 
+	// YUC1
 	public void computeUtilizationComponentsPrimary(
 			BecDefinition bec, VdypLayer vdypLayer, VolumeComputeMode volumeComputeMode,
 			CompatibilityVariableMode compatibilityVariableMode

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/EstimationMethods.java

@@ -171,7 +171,8 @@ public float primaryHeightFromLeadHeightInitial(
 	 * @throws ProcessingException
 	 */
 	public float estimateNonPrimaryLoreyHeight(
-			BaseVdypSpecies vspec, BaseVdypSpecies vspecPrime, BecDefinition bec, float leadHeight, float primaryHeight
+			BaseVdypSpecies<?> vspec, BaseVdypSpecies<?> vspecPrime, BecDefinition bec, float leadHeight,
+			float primaryHeight
 	) throws ProcessingException {
 		return estimateNonPrimaryLoreyHeight(vspec.getGenus(), vspecPrime.getGenus(), bec, leadHeight, primaryHeight);
 	}

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common_calculators/Height2SiteIndex.java

@@ -6,7 +6,6 @@
 import static ca.bc.gov.nrs.vdyp.common_calculators.enumerations.SiteIndexAgeType.SI_AT_TOTAL;
 import static ca.bc.gov.nrs.vdyp.common_calculators.enumerations.SiteIndexEstimationType.*;
 
-import java.util.function.DoubleBinaryOperator;
 import java.util.function.DoubleUnaryOperator;
 
 import ca.bc.gov.nrs.vdyp.common.Utils;

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common_calculators/SiteIndex2Height.java

@@ -7,7 +7,6 @@
 import static ca.bc.gov.nrs.vdyp.common_calculators.enumerations.SiteIndexEstimationType.SI_EST_DIRECT;
 
 import java.util.function.DoubleBinaryOperator;
-import java.util.function.DoubleUnaryOperator;
 
 import ca.bc.gov.nrs.vdyp.common.Utils;
 import ca.bc.gov.nrs.vdyp.common_calculators.custom_exceptions.CommonCalculatorException;

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/BaseVdypLayer.java

@@ -1,5 +1,6 @@
 package ca.bc.gov.nrs.vdyp.model;
 
+import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashMap;
@@ -11,12 +12,11 @@
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
-public abstract class BaseVdypLayer<S extends BaseVdypSpecies, I extends BaseVdypSite> {
+public abstract class BaseVdypLayer<S extends BaseVdypSpecies<I>, I extends BaseVdypSite> {
 
 	private final PolygonIdentifier polygonIdentifier;
 	private final LayerType layerType;
 	private LinkedHashMap<String, S> species = new LinkedHashMap<>();
-	private LinkedHashMap<String, I> sites = new LinkedHashMap<>();
 	private Optional<Integer> inventoryTypeGroup = Optional.empty();
 
 	protected BaseVdypLayer(
@@ -52,17 +52,9 @@ public void setSpecies(Collection<S> species) {
 	}
 
 	public LinkedHashMap<String, I> getSites() {
-		return sites;
-	}
-
-	public void setSites(Map<String, I> sites) {
-		this.sites.clear();
-		this.sites.putAll(sites);
-	}
-
-	public void setSites(Collection<I> sites) {
-		this.sites.clear();
-		sites.forEach(spec -> this.sites.put(spec.getSiteGenus(), spec));
+		var result = new LinkedHashMap<String, I>(species.size());
+		species.forEach((key, spec) -> spec.getSite().ifPresent(site -> result.put(key, site)));
+		return result;
 	}
 
 	public Optional<Integer> getInventoryTypeGroup() {
@@ -73,7 +65,7 @@ public void setInventoryTypeGroup(Optional<Integer> inventoryTypeGroup) {
 		this.inventoryTypeGroup = inventoryTypeGroup;
 	}
 
-	public abstract static class Builder<T extends BaseVdypLayer<S, I>, S extends BaseVdypSpecies, I extends BaseVdypSite, SB extends BaseVdypSpecies.Builder<S>, IB extends BaseVdypSite.Builder<I>>
+	public abstract static class Builder<T extends BaseVdypLayer<S, I>, S extends BaseVdypSpecies<I>, I extends BaseVdypSite, SB extends BaseVdypSpecies.Builder<S, I, IB>, IB extends BaseVdypSite.Builder<I>>
 			extends ModelClassBuilder<T> {
 		protected Optional<PolygonIdentifier> polygonIdentifier = Optional.empty();
 		protected Optional<LayerType> layerType = Optional.empty();
@@ -124,16 +116,6 @@ public Builder<T, S, I, SB, IB> addSpecies(S species) {
 			return this;
 		}
 
-		public Builder<T, S, I, SB, IB> addSite(Consumer<IB> config) {
-			siteBuilders.add(config);
-			return this;
-		}
-
-		public Builder<T, S, I, SB, IB> addSite(I site) {
-			this.sites.add(site);
-			return this;
-		}
-
 		public Builder<T, S, I, SB, IB> inventoryTypeGroup(int inventoryTypeGroup) {
 			return this.inventoryTypeGroup(Optional.of(inventoryTypeGroup));
 		}
@@ -155,37 +137,7 @@ public Builder<T, S, I, SB, IB> copy(T toCopy) {
 			return this;
 		}
 
-		public <I2 extends BaseVdypSite> Builder<T, S, I, SB, IB>
-				adaptSites(BaseVdypLayer<?, I2> toCopy, BiConsumer<IB, I2> config) {
-			toCopy.getSites().values().forEach(siteToCopy -> {
-				this.adaptSite(siteToCopy, config);
-			});
-			return this;
-		}
-
-		public <I2 extends BaseVdypSite> Builder<T, S, I, SB, IB> adaptSite(I2 toCopy, BiConsumer<IB, I2> config) {
-			this.addSite(builder -> {
-				builder.adapt(toCopy);
-				builder.polygonIdentifier = Optional.empty();
-				builder.layerType = Optional.empty();
-				config.accept(builder, toCopy);
-			});
-			return this;
-		}
-
-		public Builder<T, S, I, SB, IB> copySites(T toCopy, BiConsumer<IB, I> config) {
-			toCopy.getSites().values().forEach(siteToCopy -> {
-				this.addSite(builder -> {
-					builder.copy(siteToCopy);
-					builder.polygonIdentifier = Optional.empty();
-					builder.layerType = Optional.empty();
-					config.accept(builder, siteToCopy);
-				});
-			});
-			return this;
-		}
-
-		public <S2 extends BaseVdypSpecies> Builder<T, S, I, SB, IB>
+		public <S2 extends BaseVdypSpecies<I2>, I2 extends BaseVdypSite> Builder<T, S, I, SB, IB>
 				adaptSpecies(BaseVdypLayer<S2, ?> toCopy, BiConsumer<SB, S2> config) {
 			toCopy.getSpecies().values().forEach(speciesToCopy -> {
 				this.addSpecies(builder -> {
@@ -232,24 +184,28 @@ protected void check(Collection<String> errors) {
 
 		protected abstract S buildSpecies(Consumer<SB> config);
 
-		protected abstract I buildSite(Consumer<IB> config);
-
 		/**
 		 * Build any builders for child objects and store the results. This will clear the stored child builders.
 		 */
 		public void buildChildren() {
 			speciesBuilders.stream().map(this::buildSpecies).collect(Collectors.toCollection(() -> species));
 			speciesBuilders.clear();
-			siteBuilders.stream().map(this::buildSite).collect(Collectors.toCollection(() -> sites));
-			siteBuilders.clear();
 		}
 
 		@Override
 		protected void postProcess(T result) {
 			super.postProcess(result);
 			buildChildren();
 			result.setSpecies(species);
-			result.setSites(sites);
+		}
+
+		@Override
+		protected String getBuilderId() {
+			return MessageFormat.format(
+					"Layer {0} {1}", //
+					polygonIdentifier.map(Object::toString).orElse("N/A"), //
+					layerType.map(Object::toString).orElse("N/A") //
+			);
 		}
 
 	}

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/BaseVdypPolygon.java

@@ -1,5 +1,6 @@
 package ca.bc.gov.nrs.vdyp.model;
 
+import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.EnumMap;
 import java.util.LinkedHashMap;
@@ -12,7 +13,7 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
-public abstract class BaseVdypPolygon<L extends BaseVdypLayer<SP, SI>, PA, SP extends BaseVdypSpecies, SI extends BaseVdypSite> {
+public abstract class BaseVdypPolygon<L extends BaseVdypLayer<SP, SI>, PA, SP extends BaseVdypSpecies<SI>, SI extends BaseVdypSite> {
 
 	private PolygonIdentifier polygonIdentifier; // FIP_P/POLYDESC
 	private PA percentAvailable; // FIP_P2/PCTFLAND
@@ -107,10 +108,10 @@ protected abstract static class Builder< //
 			T extends BaseVdypPolygon<L, PA, SP, SI>, //
 			L extends BaseVdypLayer<SP, SI>, //
 			PA, //
-			SP extends BaseVdypSpecies, //
+			SP extends BaseVdypSpecies<SI>, //
 			SI extends BaseVdypSite, //
 			LB extends BaseVdypLayer.Builder<L, SP, SI, SPB, SIB>, //
-			SPB extends BaseVdypSpecies.Builder<SP>, //
+			SPB extends BaseVdypSpecies.Builder<SP, SI, SIB>, //
 			SIB extends BaseVdypSite.Builder<SI>> //
 
 			extends ModelClassBuilder<T> {
@@ -254,5 +255,13 @@ public void buildChildren() {
 			layersBuilders.clear();
 		}
 
+		@Override
+		protected String getBuilderId() {
+			return MessageFormat.format(
+					"Polygon {0}", //
+					polygonIdentifier.map(Object::toString).orElse("N/A") //
+			);
+		}
+
 	}
 }

vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/BaseVdypSite.java

@@ -1,5 +1,6 @@
 package ca.bc.gov.nrs.vdyp.model;
 
+import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.Optional;
 
@@ -173,6 +174,16 @@ protected void check(Collection<String> errors) {
 			requirePresent(siteGenus, "siteGenus", errors);
 		}
 
+		@Override
+		protected String getBuilderId() {
+			return MessageFormat.format(
+					"Site {0} {1} {2}", //
+					polygonIdentifier.map(Object::toString).orElse("N/A"), //
+					layerType.map(Object::toString).orElse("N/A"), //
+					siteGenus.map(Object::toString).orElse("N/A")//
+			);
+		}
+
 	}
 
 }