Parsing layer-species data file

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/AbstractStreamingParser.java

@@ -32,7 +32,7 @@ public T next() throws IOException, ResourceParseException {
 	 *
 	 * @return
 	 */
-	protected abstract T convert(Map<String, Object> entry);
+	protected abstract T convert(Map<String, Object> entry) throws ResourceParseException;
 
 	@Override
 	public boolean hasNext() throws IOException, ResourceParseException {

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/BaseCoefficientParser.java

@@ -117,7 +117,7 @@ public BaseCoefficientParser<T, M> groupIndexKey(int maxGroups) {
 
 	public BaseCoefficientParser<T, M> speciesKey(String name) {
 		return key(
-				2, name, ControlledValueParser.SPECIES, SP0DefinitionParser::getSpeciesAliases,
+				2, name, ControlledValueParser.GENUS, GenusDefinitionParser::getSpeciesAliases,
 				"%s is not a valid species"
 		);
 	}

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/ControlledValueParser.java

@@ -1,8 +1,10 @@
 package ca.bc.gov.nrs.vdyp.io.parse;
 
 import java.util.Map;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.function.BiFunction;
+import java.util.function.Predicate;
 
 @FunctionalInterface
 public interface ControlledValueParser<T> {
@@ -30,6 +32,7 @@ public interface ControlledValueParser<T> {
 	public static <U> ControlledValueParser<U> validate(
 			ControlledValueParser<U> delegate, BiFunction<U, Map<String, Object>, Optional<String>> validator
 	) {
+		Objects.requireNonNull(delegate, "delegate must not be null");
 		return (s, c) -> {
 			var value = delegate.parse(s, c);
 			var error = validator.apply(value, c);
@@ -47,23 +50,64 @@ public static <U> ControlledValueParser<U> validate(
 	 * @param delegate Parser to use if the string is not blank
 	 */
 	public static <U> ControlledValueParser<Optional<U>> optional(ControlledValueParser<U> delegate) {
+		Objects.requireNonNull(delegate, "delegate must not be null");
+		return pretestOptional(delegate, s -> !s.isBlank());
+	}
+
+	/**
+	 * Makes a parser that parses if the string passes the test, and returns an
+	 * empty Optional otherwise.
+	 *
+	 * @param delegate Parser to use if the string is not blank
+	 * @param test     Test to apply to the string
+	 */
+	public static <U> ControlledValueParser<Optional<U>>
+			pretestOptional(ControlledValueParser<U> delegate, Predicate<String> test) {
+		Objects.requireNonNull(delegate, "delegate must not be null");
 		return (s, c) -> {
-			if (!s.isBlank()) {
+			if (test.test(s)) {
 				return Optional.of(delegate.parse(s, c));
 			}
 			return Optional.empty();
 		};
 	}
 
 	/**
-	 * Parser that strips whitespace and validates that the string is a Species ID
+	 * Makes a parser that parses the string, then tests it, and returns empty if it
+	 * fails.
+	 *
+	 * @param delegate Parser to use
+	 * @param test     Test to apply to the parsed result
+	 */
+	public static <U> ControlledValueParser<Optional<U>>
+			posttestOptional(ControlledValueParser<U> delegate, Predicate<U> test) {
+		Objects.requireNonNull(delegate, "delegate must not be null");
+		return (s, c) -> {
+			var result = delegate.parse(s, c);
+			if (test.test(result)) {
+				return Optional.of(result);
+			}
+			return Optional.empty();
+		};
+	}
+
+	/**
+	 * Parser that strips whitespace and validates that the string is a Genus (SP0)
+	 * ID
 	 */
-	static final ControlledValueParser<String> SPECIES = (string, control) -> {
+	static final ControlledValueParser<String> GENUS = (string, control) -> {
 		var result = string.strip();
-		SP0DefinitionParser.checkSpecies(control, result);
+		GenusDefinitionParser.checkSpecies(control, result);
 		return result;
 	};
 
+	/**
+	 * Parser that strips whitespace of a Species (SP64) id
+	 */
+	// Currently just parses as a string but marking it explicitly makes it clearer
+	// and could allow for validation later.
+	public static final ControlledValueParser<String> SPECIES = (s, c) -> s.strip();
+
 	/**
 	 * Parser that strips whitespace and validates that the string is a BEC ID
 	 */

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/EquationGroupParser.java

@@ -37,7 +37,7 @@ public EquationGroupParser(int identifierLength) {
 	public Map<String, Map<String, Integer>> parse(InputStream is, Map<String, Object> control)
 			throws IOException, ResourceParseException {
 
-		final var sp0List = SP0DefinitionParser.getSpecies(control);
+		final var sp0List = GenusDefinitionParser.getSpecies(control);
 
 		var becKeys = BecDefinitionParser.getBecAliases(control);
 
@@ -70,7 +70,7 @@ public Map<String, Map<String, Integer>> parse(InputStream is, Map<String, Objec
 
 		List<String> errors = new ArrayList<>();
 
-		var sp0Keys = SP0DefinitionParser.getSpeciesAliases(control);
+		var sp0Keys = GenusDefinitionParser.getSpeciesAliases(control);
 
 		var restrictedBecKeys = becKeys.stream().filter(k -> !hiddenBecs.contains(k)).toList();
 

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/SP0DefinitionParser.java → vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/GenusDefinitionParser.java

@@ -9,15 +9,15 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import ca.bc.gov.nrs.vdyp.model.SP0Definition;
+import ca.bc.gov.nrs.vdyp.model.GenusDefinition;
 
 /**
- * Parser for a SP0 Definition data file
+ * Parser for a Genus (SP0) Definition data file
  *
  * @author Kevin Smith, Vivid Solutions
  *
  */
-public class SP0DefinitionParser implements ControlMapSubResourceParser<List<SP0Definition>> {
+public class GenusDefinitionParser implements ControlMapSubResourceParser<List<GenusDefinition>> {
 
 	public static final String CONTROL_KEY = "SP0_DEF";
 
@@ -30,28 +30,28 @@ public class SP0DefinitionParser implements ControlMapSubResourceParser<List<SP0
 							.flatMap(v -> v == 0 ? Optional.empty() : Optional.of(v))
 			);
 
-	public SP0DefinitionParser() {
+	public GenusDefinitionParser() {
 		super();
 		this.num_sp0 = 16;
 	}
 
-	public SP0DefinitionParser(int num_sp0) {
+	public GenusDefinitionParser(int num_sp0) {
 		super();
 		this.num_sp0 = num_sp0;
 	}
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public List<SP0Definition> parse(InputStream is, Map<String, Object> control)
+	public List<GenusDefinition> parse(InputStream is, Map<String, Object> control)
 			throws IOException, ResourceParseException {
-		SP0Definition[] result = new SP0Definition[num_sp0];
+		GenusDefinition[] result = new GenusDefinition[num_sp0];
 		result = lineParser.parse(is, result, (v, r) -> {
 			String alias = (String) v.get("alias");
 			Optional<Integer> preference = (Optional<Integer>) v.get("preference");
 			String name = (String) v.get("name");
 			Integer lineNumber = (Integer) v.get(LineParser.LINE_NUMBER_KEY);
 
-			var defn = new SP0Definition(alias, preference, name);
+			var defn = new GenusDefinition(alias, preference, name);
 			int p = preference.orElse(lineNumber);
 
 			if (p > num_sp0) {
@@ -80,7 +80,7 @@ public List<SP0Definition> parse(InputStream is, Map<String, Object> control)
 
 	public static void checkSpecies(final List<String> speciesIndicies, final String sp0) throws ValueParseException {
 		if (!speciesIndicies.contains(sp0)) {
-			throw new ValueParseException(sp0, sp0 + " is not a valid species");
+			throw new ValueParseException(sp0, sp0 + " is not a valid genus (SP0)");
 		}
 	}
 
@@ -89,13 +89,13 @@ public static void checkSpecies(final Map<String, Object> controlMap, final Stri
 		checkSpecies(speciesIndicies, sp0);
 	}
 
-	public static List<SP0Definition> getSpecies(final Map<String, Object> controlMap) {
+	public static List<GenusDefinition> getSpecies(final Map<String, Object> controlMap) {
 		return ResourceParser
-				.<List<SP0Definition>>expectParsedControl(controlMap, SP0DefinitionParser.CONTROL_KEY, List.class);
+				.<List<GenusDefinition>>expectParsedControl(controlMap, GenusDefinitionParser.CONTROL_KEY, List.class);
 	}
 
 	public static List<String> getSpeciesAliases(final Map<String, Object> controlMap) {
-		return getSpecies(controlMap).stream().map(SP0Definition::getAlias).collect(Collectors.toList());
+		return getSpecies(controlMap).stream().map(GenusDefinition::getAlias).collect(Collectors.toList());
 	}
 
 	/**
@@ -105,7 +105,7 @@ public static List<String> getSpeciesAliases(final Map<String, Object> controlMa
 	 * @param controlMap
 	 * @return
 	 */
-	public static SP0Definition getSpeciesByIndex(final int index, final Map<String, Object> controlMap) {
+	public static GenusDefinition getSpeciesByIndex(final int index, final Map<String, Object> controlMap) {
 
 		return getSpecies(controlMap).get(index - 1);
 	}

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/HLCoefficientParser.java

@@ -54,7 +54,7 @@ public boolean isStopLine(String line) {
 	public MatrixMap2<String, Region, Coefficients> parse(InputStream is, Map<String, Object> control)
 			throws IOException, ResourceParseException {
 		final var regionIndicies = Arrays.asList(Region.values());
-		final var speciesIndicies = SP0DefinitionParser.getSpeciesAliases(control);
+		final var speciesIndicies = GenusDefinitionParser.getSpeciesAliases(control);
 
 		MatrixMap2<String, Region, Coefficients> result = new MatrixMap2Impl<String, Region, Coefficients>(
 				speciesIndicies, regionIndicies

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/HLNonprimaryCoefficientParser.java

@@ -50,7 +50,7 @@ public boolean isStopLine(String line) {
 	public MatrixMap3<String, String, Region, NonprimaryHLCoefficients>
 			parse(InputStream is, Map<String, Object> control) throws IOException, ResourceParseException {
 		final var regionIndicies = Arrays.asList(Region.values());
-		final var speciesIndicies = SP0DefinitionParser.getSpeciesAliases(control);
+		final var speciesIndicies = GenusDefinitionParser.getSpeciesAliases(control);
 
 		MatrixMap3<String, String, Region, NonprimaryHLCoefficients> result = new MatrixMap3Impl<String, String, Region, NonprimaryHLCoefficients>(
 				speciesIndicies, speciesIndicies, regionIndicies
@@ -62,8 +62,8 @@ public boolean isStopLine(String line) {
 			var region = (Region) v.get(REGION_KEY);
 			@SuppressWarnings("unchecked")
 			var coefficients = (List<Float>) v.get(COEFFICIENT_KEY);
-			SP0DefinitionParser.checkSpecies(speciesIndicies, sp0_1);
-			SP0DefinitionParser.checkSpecies(speciesIndicies, sp0_2);
+			GenusDefinitionParser.checkSpecies(speciesIndicies, sp0_1);
+			GenusDefinitionParser.checkSpecies(speciesIndicies, sp0_2);
 
 			if (coefficients.size() < NUM_COEFFICIENTS) {
 				throw new ValueParseException(null, "Expected 2 coefficients"); // TODO handle this better

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/SiteCurveParser.java

@@ -42,7 +42,7 @@ public Map<String, SiteCurve> parse(InputStream is, Map<String, Object> control)
 
 			return r;
 		}, control);
-		final var sp0List = SP0DefinitionParser.getSpeciesAliases(control);
+		final var sp0List = GenusDefinitionParser.getSpeciesAliases(control);
 
 		var missing = ExpectationDifference.difference(result.keySet(), sp0List).getMissing();
 		if (!missing.isEmpty()) {

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/UpperCoefficientParser.java

@@ -45,7 +45,7 @@ public MatrixMap3<Region, String, Integer, Float> parse(InputStream is, Map<Stri
 			throws IOException, ResourceParseException {
 		var regionIndicies = Arrays.asList(Region.values());
 		List<Integer> coeIndicies = Stream.iterate(1, x -> x + 1).limit(NUM_COEFFICIENTS).collect(Collectors.toList());
-		final var speciesIndicies = SP0DefinitionParser.getSpeciesAliases(control);
+		final var speciesIndicies = GenusDefinitionParser.getSpeciesAliases(control);
 
 		MatrixMap3<Region, String, Integer, Float> result = new MatrixMap3Impl<Region, String, Integer, Float>(
 				regionIndicies, speciesIndicies, coeIndicies

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/UtilComponentParser.java

@@ -43,7 +43,7 @@ public boolean isStopLine(String line) {
 	public MatrixMap3<Integer, String, String, Coefficients> parse(InputStream is, Map<String, Object> control)
 			throws IOException, ResourceParseException {
 		final var becIndices = BecDefinitionParser.getBecAliases(control);
-		final var speciesIndicies = SP0DefinitionParser.getSpeciesAliases(control);
+		final var speciesIndicies = GenusDefinitionParser.getSpeciesAliases(control);
 		final var ucIndices = Arrays.asList(1, 2, 3, 4);
 
 		MatrixMap3<Integer, String, String, Coefficients> result = new MatrixMap3Impl<Integer, String, String, Coefficients>(
@@ -61,7 +61,7 @@ public MatrixMap3<Integer, String, String, Coefficients> parse(InputStream is, M
 
 			@SuppressWarnings("unchecked")
 			var coefficients = (List<Float>) v.get(COEFFICIENT_KEY);
-			SP0DefinitionParser.checkSpecies(speciesIndicies, sp0);
+			GenusDefinitionParser.checkSpecies(speciesIndicies, sp0);
 
 			if (coefficients.size() < numCoefficients) {
 				throw new ValueParseException(null, "Expected " + numCoefficients + " coefficients");

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/ValueParser.java

@@ -121,6 +121,44 @@ public static ValueParser<Integer> indexParser(String sequenceName, int indexFro
 	 */
 	public static final ValueParser<Float> FLOAT = numberParser(Float::parseFloat, Float.class);
 
+	/**
+	 * Parser for percentages
+	 */
+	public static final ValueParser<Float> PERCENTAGE = ValueParser
+			.range(FLOAT, 0.0f, true, 100.0f, true, "Percentage");
+
+	/**
+	 * Validate that a parsed value is within a range
+	 *
+	 * @param parser     underlying parser
+	 * @param min        the lower bound
+	 * @param includeMin is the lower bound inclusive
+	 * @param max        the upper bound
+	 * @param includeMax is the upper bound inclusive
+	 * @param name       Name for the value to use in the parse error if it is out
+	 *                   of the range.
+	 */
+	public static <T extends Comparable<T>> ValueParser<T>
+			range(ValueParser<T> parser, T min, boolean includeMin, T max, boolean includeMax, String name) {
+		return validate(parser, x -> {
+			if (x.compareTo(min) < (includeMin ? 0 : 1)) {
+				return Optional.of(
+						String.format(
+								"%s must be %s %s.", name, includeMin ? "greater than or equal to" : "greater than", min
+						)
+				);
+			}
+			if (x.compareTo(max) > (includeMax ? 0 : -1)) {
+				return Optional.of(
+						String.format(
+								"%s must be %s %s.", name, includeMax ? "less than or equal to" : "less than", max
+						)
+				);
+			}
+			return Optional.empty();
+		});
+	}
+
 	/**
 	 * Parser for integers as booleans
 	 */
@@ -186,6 +224,28 @@ public static <U> ValueParser<Optional<U>> optional(ValueParser<U> delegate) {
 		return uncontrolled(ControlledValueParser.optional(delegate));
 	}
 
+	/**
+	 * Makes a parser that parses if the string passes the test, and returns an
+	 * empty Optional otherwise.
+	 *
+	 * @param delegate Parser to use if the string is not blank
+	 * @param test     Test to apply to the string
+	 */
+	public static <U> ValueParser<Optional<U>> pretestOptional(ValueParser<U> delegate, Predicate<String> test) {
+		return uncontrolled(ControlledValueParser.pretestOptional(delegate, test));
+	}
+
+	/**
+	 * Makes a parser that parses the string, then tests it, and returns empty if it
+	 * fails.
+	 *
+	 * @param delegate Parser to use
+	 * @param test     Test to apply to the parsed result
+	 */
+	public static <U> ValueParser<Optional<U>> posttestOptional(ValueParser<U> delegate, Predicate<U> test) {
+		return uncontrolled(ControlledValueParser.posttestOptional(delegate, test));
+	}
+
 	/**
 	 * Parse a string as a set of fixed length chucks.
 	 *

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/VeteranDQParser.java

@@ -41,7 +41,7 @@ public boolean isStopLine(String line) {
 	@Override
 	public MatrixMap2<String, Region, Coefficients> parse(InputStream is, Map<String, Object> control)
 			throws IOException, ResourceParseException {
-		final var speciesIndicies = SP0DefinitionParser.getSpeciesAliases(control);
+		final var speciesIndicies = GenusDefinitionParser.getSpeciesAliases(control);
 		final var regionIndicies = Arrays.asList(Region.values());
 
 		MatrixMap2<String, Region, Coefficients> result = new MatrixMap2Impl<String, Region, Coefficients>(
@@ -54,7 +54,7 @@ public MatrixMap2<String, Region, Coefficients> parse(InputStream is, Map<String
 
 			@SuppressWarnings("unchecked")
 			var coefficients = (List<Float>) v.get(COEFFICIENT_KEY);
-			SP0DefinitionParser.checkSpecies(speciesIndicies, sp0);
+			GenusDefinitionParser.checkSpecies(speciesIndicies, sp0);
 
 			if (coefficients.size() < numCoefficients) {
 				throw new ValueParseException(null, "Expected " + numCoefficients + " coefficients");

vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/model/SP0Definition.java → vdyp-core/src/main/java/ca/bc/gov/nrs/vdyp/model/GenusDefinition.java

@@ -2,11 +2,11 @@
 
 import java.util.Optional;
 
-public class SP0Definition extends AbstractSpeciesDefinition {
+public class GenusDefinition extends AbstractSpeciesDefinition {
 
 	final Optional<Integer> preference;
 
-	public SP0Definition(String alias, Optional<Integer> preference, String name) {
+	public GenusDefinition(String alias, Optional<Integer> preference, String name) {
 		super(alias, name);
 		this.preference = preference;
 	}