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;
  }