Fix warnings and code smells

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

@@ -34,7 +34,7 @@ public static <U> ExpectationDifference<U> difference(Collection<U> values, Coll
 		missing.removeAll(values);
 		var unexpected = new HashSet<U>(values);
 		unexpected.removeAll(expected);
-		return new ExpectationDifference<U>(missing, unexpected);
+		return new ExpectationDifference<>(missing, unexpected);
 	}
 
 	/**

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

@@ -88,7 +88,7 @@ public <T> T handle(Function<Value, T> valueHandler, Function<Marker, T> markerH
 	 * @return
 	 */
 	public static <Value, Marker> Builder<Value, Marker> builder(Class<Value> vClazz, Class<Marker> mClazz) {
-		return new Builder<Value, Marker>();
+		return new Builder<>();
 	}
 
 	/**
@@ -102,22 +102,18 @@ public static <Value, Marker> Builder<Value, Marker> builder(Class<Value> vClazz
 	 */
 	public static class Builder<Value, Marker> {
 
-		public Builder() {
-
-		}
-
 		/**
 		 * Create a ValueOrMarker with a Marker
 		 */
 		public ValueOrMarker<Value, Marker> marker(Marker m) {
-			return new ValueOrMarker<Value, Marker>(m, true);
+			return new ValueOrMarker<>(m, true);
 		}
 
 		/**
 		 * Create a ValueOrMarker with a Value
 		 */
 		public ValueOrMarker<Value, Marker> value(Value v) {
-			return new ValueOrMarker<Value, Marker>(v, false);
+			return new ValueOrMarker<>(v, false);
 		}
 	}
 }

vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/GenusDefinitionParser.java

@@ -7,7 +7,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import java.util.stream.Collectors;
 
 import ca.bc.gov.nrs.vdyp.common.Utils;
 import ca.bc.gov.nrs.vdyp.model.GenusDefinition;
@@ -60,9 +59,9 @@ public GenusDefinitionParser() {
 		this.numSp0 = 16;
 	}
 
-	public GenusDefinitionParser(int num_sp0) {
+	public GenusDefinitionParser(int numSp0) {
 		super();
-		this.numSp0 = num_sp0;
+		this.numSp0 = numSp0;
 	}
 
 	@SuppressWarnings("unchecked")

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

@@ -1,7 +1,6 @@
 package ca.bc.gov.nrs.vdyp.model;
 
 import java.util.Collection;
-import java.util.Collections;
 import java.util.EnumMap;
 import java.util.LinkedHashMap;
 import java.util.LinkedList;

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

@@ -11,7 +11,7 @@ public enum UtilizationClass {
 	OVER225(4, ">22.5 cm", 22.5f, 10000f);
 
 	public final int index;
-	public final String name;
+	public final String className;
 	public final float lowBound;
 	public final float highBound;
 
@@ -25,9 +25,9 @@ public enum UtilizationClass {
 		}
 	}
 
-	UtilizationClass(int index, String name, float lowBound, float highBound) {
+	UtilizationClass(int index, String className, float lowBound, float highBound) {
 		this.index = index;
-		this.name = name;
+		this.className = className;
 		this.lowBound = lowBound;
 		this.highBound = highBound;
 	}

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

@@ -1,6 +1,5 @@
 package ca.bc.gov.nrs.vdyp.model;
 
-import java.util.Arrays;
 import java.util.Optional;
 import java.util.function.Consumer;
 

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

@@ -33,7 +33,9 @@ public <O extends BaseVdypPolygon<?, U>, U> VdypPolygon(O toCopy, Function<U, Fl
 
 	@Computed
 	public int getInventoryTypeGroup() {
-		return this.getLayers().get(LayerType.PRIMARY).getInventoryTypeGroup().get();
+		return this.getLayers().get(LayerType.PRIMARY).getInventoryTypeGroup().orElseThrow(
+				() -> new IllegalArgumentException("Inventory Type Group does not exist if there is no primary layer")
+		);
 	}
 
 	@Computed

vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/io/parse/BecDefinitionParserTest.java

@@ -5,22 +5,15 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.allOf;
 import static org.hamcrest.Matchers.hasProperty;
-import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.sameInstance;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-import java.util.ArrayList;
 import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-
 import static org.hamcrest.Matchers.equalTo;
 
 import org.hamcrest.Matchers;
 import org.junit.jupiter.api.Test;
 
-import ca.bc.gov.nrs.vdyp.model.BecDefinition;
-import ca.bc.gov.nrs.vdyp.model.BecLookup;
 import ca.bc.gov.nrs.vdyp.model.Region;
 import ca.bc.gov.nrs.vdyp.test.TestUtils;
 

vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/io/parse/ValueParserTest.java

@@ -1,13 +1,9 @@
 package ca.bc.gov.nrs.vdyp.io.parse;
 
-import static ca.bc.gov.nrs.vdyp.common.Utils.constMap;
-import static ca.bc.gov.nrs.vdyp.test.VdypMatchers.isMarker;
-import static ca.bc.gov.nrs.vdyp.test.VdypMatchers.isValue;
 import static ca.bc.gov.nrs.vdyp.test.VdypMatchers.notPresent;
 import static ca.bc.gov.nrs.vdyp.test.VdypMatchers.present;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.aMapWithSize;
-import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.hasEntry;
 import static org.hamcrest.Matchers.hasProperty;
 import static org.hamcrest.Matchers.is;
@@ -19,7 +15,6 @@
 
 import org.junit.jupiter.api.Test;
 
-import ca.bc.gov.nrs.vdyp.common.Utils;
 import ca.bc.gov.nrs.vdyp.model.LayerType;
 
 class ValueParserTest {

vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/io/write/VriAdjustInputWriterTest.java

@@ -7,19 +7,14 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.util.Collections;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
-import java.util.Optional;
-
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 import ca.bc.gov.nrs.vdyp.common.ControlKeys;
 import ca.bc.gov.nrs.vdyp.common.Utils;
 import ca.bc.gov.nrs.vdyp.io.FileResolver;
-import ca.bc.gov.nrs.vdyp.model.Coefficients;
 import ca.bc.gov.nrs.vdyp.model.FipMode;
 import ca.bc.gov.nrs.vdyp.model.LayerType;
 import ca.bc.gov.nrs.vdyp.model.VdypLayer;

vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/model/FipModeTest.java

@@ -12,22 +12,22 @@
 class FipModeTest {
 
 	@ParameterizedTest()
-	@EnumSource(FipMode.class) 
-	void testGetByCodeExpected(FipMode mode){
+	@EnumSource(FipMode.class)
+	void testGetByCodeExpected(FipMode mode) {
 		var result = FipMode.getByCode(mode.getCode());
 		assertThat(result, present(is(mode)));
 	}
-	
+
 	@ParameterizedTest()
-	@ValueSource(ints= {-2, Integer.MIN_VALUE, Integer.MAX_VALUE, 42}) 
-	void testGetByCodeUnexpected(int code){
+	@ValueSource(ints = { -2, Integer.MIN_VALUE, Integer.MAX_VALUE, 42 })
+	void testGetByCodeUnexpected(int code) {
 		var result = FipMode.getByCode(code);
 		assertThat(result, present(is(FipMode.DONT_PROCESS)));
 	}
-	
+
 	@ParameterizedTest()
-	@ValueSource(ints= {0}) 
-	void testGetByCodeMissing(int code){
+	@ValueSource(ints = { 0 })
+	void testGetByCodeMissing(int code) {
 		var result = FipMode.getByCode(code);
 		assertThat(result, notPresent());
 	}

vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/model/VdypPolygonTest.java

@@ -5,7 +5,6 @@
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
 import org.easymock.EasyMock;
-import org.hamcrest.Matchers;
 import org.junit.jupiter.api.Test;
 
 class VdypPolygonTest {

vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/model/VdypSpeciesTest.java

@@ -4,7 +4,6 @@
 import static org.hamcrest.Matchers.*;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-import org.easymock.EasyMock;
 import org.junit.jupiter.api.Test;
 
 class VdypSpeciesTest {

vdyp-fip/src/main/java/ca/bc/gov/nrs/vdyp/fip/FipStart.java

@@ -366,14 +366,13 @@ VdypPolygon createVdypPolygon(FipPolygon fipPolygon, Map<LayerType, VdypLayer> p
 
 		float percentAvailable = estimatePercentForestLand(fipPolygon, fipVetLayer, fipPrimaryLayer);
 
-		var vdypPolygon = VdypPolygon.build(builder -> {
-			builder.copy(fipPolygon, (x) -> percentAvailable);
-		});
+		var vdypPolygon = VdypPolygon.build(builder -> builder.copy(fipPolygon, x -> percentAvailable));
 		vdypPolygon.setLayers(processedLayers);
 		return vdypPolygon;
 	}
 
 	// FIPLAND
+	@SuppressWarnings("java:S3655")
 	float estimatePercentForestLand(FipPolygon fipPolygon, FipLayer fipVetLayer, FipLayerPrimary fipPrimaryLayer)
 			throws ProcessingException {
 		if (fipPolygon.getPercentAvailable().isPresent()) {
@@ -1575,6 +1574,7 @@ void reconcileComponents(
 	private static final List<UtilizationClass> MODE_1_RECONCILE_AVAILABILITY_CLASSES = List
 			.of(UtilizationClass.OVER225, UtilizationClass.U175TO225, UtilizationClass.U125TO175);
 
+	@SuppressWarnings("java:S3655")
 	void reconcileComponentsMode1(
 			Coefficients baseAreaUtil, Coefficients treesPerHectareUtil, Coefficients quadMeanDiameterUtil,
 			float tphSumHigh
@@ -1741,6 +1741,7 @@ private void reconcileComponentsMode2(
 		}
 	}
 
+	@SuppressWarnings("java:S3655")
 	void reconcileComponentsMode3(
 			Coefficients baseAreaUtil, Coefficients treesPerHectareUtil, Coefficients quadMeanDiameterUtil
 	) {
@@ -1825,7 +1826,7 @@ void estimateQuadMeanDiameterByUtilization(BecDefinition bec, Coefficients quadM
 		float quadMeanDiameter07 = quadMeanDiameterUtil.getCoe(UTIL_ALL);
 
 		for (var uc : UTIL_CLASSES) {
-			log.atDebug().setMessage("For util level {}").addArgument(uc.name);
+			log.atDebug().setMessage("For util level {}").addArgument(uc.className);
 			final var coeMap = Utils.<MatrixMap3<Integer, String, String, Coefficients>>expectParsedControl(
 					controlMap, UtilComponentDQParser.CONTROL_KEY, MatrixMap3.class
 			);
@@ -1876,15 +1877,17 @@ void estimateQuadMeanDiameterByUtilization(BecDefinition bec, Coefficients quadM
 				throw new IllegalStateException(
 						"Should not be attempting to process small component or all large components"
 				);
+			default:
+				throw new IllegalStateException("Unknown utilization class " + uc);
 			}
 
-			log.atDebug().setMessage("Util DQ for class {} is {}").addArgument(uc.name)
+			log.atDebug().setMessage("Util DQ for class {} is {}").addArgument(uc.className)
 					.addArgument(quadMeanDiameterUtil.getCoe(uc.index));
 		}
 
 		log.atTrace().setMessage("Estimated Diameters {}").addArgument(
 				() -> UTIL_CLASSES.stream()
-						.map(uc -> String.format("%s: %d", uc.name, quadMeanDiameterUtil.getCoe(uc.index)))
+						.map(uc -> String.format("%s: %d", uc.className, quadMeanDiameterUtil.getCoe(uc.index)))
 		);
 
 	}
@@ -1915,15 +1918,14 @@ List<FipSpecies> findPrimarySpecies(Map<String, FipSpecies> allSpecies) {
 		// Start with a deep copy of the species map so there are no side effects from
 		// the manipulation this method does.
 		var combined = new HashMap<String, FipSpecies>(allSpecies.size());
-		allSpecies.entrySet().stream().forEach(spec -> {
-			combined.put(spec.getKey(), new FipSpecies(spec.getValue()));
-		});
+		allSpecies.entrySet().stream().forEach(spec -> combined.put(spec.getKey(), new FipSpecies(spec.getValue())));
 
 		for (var combinationGroup : PRIMARY_SPECIES_TO_COMBINE) {
 			var groupSpecies = combinationGroup.stream().map(combined::get).filter(Objects::nonNull).toList();
 			if (groupSpecies.size() < 2) {
 				continue;
 			}
+			@SuppressWarnings("java:S3655")
 			var groupPrimary = new FipSpecies(groupSpecies.stream().sorted(PERCENT_GENUS_DESCENDING).findFirst().get());
 			var total = (float) groupSpecies.stream().mapToDouble(FipSpecies::getPercentGenus).sum();
 			combinationGroup.forEach(combined::remove);
@@ -2522,9 +2524,7 @@ float normalizeUtilizationComponents(Coefficients components) throws ProcessingE
 		if (sum <= 0f) {
 			throw new ProcessingException("Total volume " + sum + " was not positive.");
 		}
-		UTIL_CLASSES.forEach(uc -> {
-			components.setCoe(uc.index, components.getCoe(uc.index) * k);
-		});
+		UTIL_CLASSES.forEach(uc -> components.setCoe(uc.index, components.getCoe(uc.index) * k));
 		return k;
 	}
 
@@ -3052,7 +3052,9 @@ public void estimateSmallComponents(FipPolygon fPoly, VdypLayer layer) {
 		float treesPerHectareSum = 0f;
 		float volumeSum = 0f;
 
-		Region region = BecDefinitionParser.getBecs(controlMap).get(fPoly.getBiogeoclimaticZone()).get().getRegion();
+		Region region = BecDefinitionParser.getBecs(controlMap).get(fPoly.getBiogeoclimaticZone())
+				.orElseThrow(() -> new IllegalStateException("Could not find BEC " + fPoly.getBiogeoclimaticZone()))
+				.getRegion();
 
 		for (VdypSpecies spec : layer.getSpecies().values()) {
 			float loreyHeightSpec = spec.getLoreyHeightByUtilization().getCoe(UTIL_ALL); // HLsp

vdyp-fip/src/main/java/ca/bc/gov/nrs/vdyp/fip/model/FipLayer.java

@@ -74,19 +74,25 @@ public void setYearsToBreastHeightSafe(float yearsToBreastHeight) {
 
 	@Override
 	public void setAgeTotal(Optional<Float> ageTotal) {
-		ageTotal.orElseThrow(() -> new IllegalArgumentException());
+		if(ageTotal.isEmpty()) {
+			throw new IllegalArgumentException("ageTotal must not be empty");
+		}
 		super.setAgeTotal(ageTotal);
 	}
 
 	@Override
 	public void setHeight(Optional<Float> height) {
-		height.orElseThrow(() -> new IllegalArgumentException());
+		if(height.isEmpty()) {
+			throw new IllegalArgumentException("height must not be empty");
+		}
 		super.setHeight(height);
 	}
 
 	@Override
 	public void setYearsToBreastHeight(Optional<Float> yearsToBreastHeight) {
-		yearsToBreastHeight.orElseThrow(() -> new IllegalArgumentException());
+		if(yearsToBreastHeight.isEmpty()) {
+			throw new IllegalArgumentException("yearsToBreastHeight must not be empty");
+		}
 		super.setYearsToBreastHeight(yearsToBreastHeight);
 	}
 

vdyp-fip/src/test/java/ca/bc/gov/nrs/vdyp/fip/FipStartTest.java

@@ -38,7 +38,6 @@
 
 import org.easymock.EasyMock;
 import org.easymock.IMocksControl;
-import org.easymock.bytebuddy.agent.builder.AgentBuilder;
 import org.hamcrest.Description;
 import org.hamcrest.Matcher;
 import org.hamcrest.Matchers;

vdyp-fip/src/test/java/ca/bc/gov/nrs/vdyp/fip/RootFinderTest.java

@@ -5,7 +5,6 @@
 import static org.hamcrest.Matchers.contains;
 
 import java.util.Arrays;
-import java.util.LinkedHashMap;
 import java.util.Map;
 import org.apache.commons.math3.analysis.MultivariateMatrixFunction;
 import org.apache.commons.math3.analysis.MultivariateVectorFunction;