Add biomass test to POSEIDON

POSEIDON/src/test/java/uk/ac/ox/oxfish/biology/tuna/EpoBiologyOnlyScenarioAllSpeciesTest.java

@@ -0,0 +1,117 @@
+package uk.ac.ox.oxfish.biology.tuna;
+
+import com.google.common.collect.ImmutableMap;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import uk.ac.ox.oxfish.biology.Species;
+import uk.ac.ox.oxfish.geography.currents.CurrentPatternMapSupplier;
+import uk.ac.ox.oxfish.model.FishState;
+import uk.ac.ox.oxfish.model.scenario.EpoAbundanceScenario;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import static uk.ac.ox.oxfish.utility.csv.CsvParserUtil.recordStream;
+
+/**
+ * Test to see if the simulated biomass is the same as the expected biomass for the first 4 quarters.
+ * Expected biomasses are generated in the preprocessing pipeline as "biomass_test.csv".
+ */
+public class EpoBiologyOnlyScenarioAllSpeciesTest {
+
+    private final Path testInputs = Paths.get(
+        "inputs", "epo_inputs", "tests"
+    );
+
+    private final Path biologyTestFile = testInputs.resolve("biomass_test.csv");
+
+    @Test
+    public void testRunBiologyOnlyScenario() {
+        final EpoAbundanceScenario scenario = new EpoAbundanceScenario();
+
+        final FishState fishState = new FishState();
+        fishState.setScenario(scenario);
+        scenario.getFadMap().setCurrentPatternMapSupplier(CurrentPatternMapSupplier.EMPTY);
+
+        fishState.start();
+
+        System.out.println("SeaTiles: " + fishState.getMap().getAllSeaTiles().size());
+
+        final Species bet = fishState.getSpecies("Bigeye tuna");
+        final Species yft = fishState.getSpecies("Yellowfin tuna");
+        final Species skj = fishState.getSpecies("Skipjack tuna");
+
+
+        System.out.println("breakpoint");
+
+        Map<Integer, Map<String, Double>> expectedBiomass = recordStream(biologyTestFile)
+            .collect(Collectors.groupingBy(
+                record -> record.getInt("day"),
+                Collectors.toMap(record -> record.getString("species"), record -> record.getDouble("biomass"))
+            ));
+
+        Map<Species, double[][]> speciesAbundances =
+            ImmutableMap.of(
+                bet, fishState.getTotalAbundance(bet),
+                yft, fishState.getTotalAbundance(yft),
+                skj, fishState.getTotalAbundance(skj)
+            );
+
+        Map<Species, double[][]> speciesDeaths =
+            ImmutableMap.of(
+                bet, fishState.getTotalAbundance(bet),
+                yft, fishState.getTotalAbundance(yft),
+                skj, fishState.getTotalAbundance(skj)
+            );
+
+        System.out.println("File found, start stepping model");
+
+        do {
+            System.out.println(fishState.getStep());
+            if (expectedBiomass.containsKey(fishState.getStep())) {
+                speciesAbundances.forEach((s, abundance) -> {
+                    System.out.println(fishState.getStep() + " " + fishState.getTotalBiomass(s) / 1000);
+                    System.out.println("Estimated biomass");
+                    Assertions.assertEquals(
+                        expectedBiomass.get(fishState.getStep()).get(s.getCode()),
+                        fishState.getTotalBiomass(s),
+                        1000000
+                    );
+                });
+            }
+                    /*System.out.println(fishState.getStep() + " " + fishState.getTotalBiomass(yft) / 1000);
+                    final double[][] totalAbundanceYFT = fishState.getTotalAbundance(yft);
+                    for (int i = 0; i < totalAbundanceYFT.length; i++) {
+                        for (int j = 0; j < totalAbundanceYFT[0].length - 1; j++) {
+
+                            deaths[i][j] = prevAbundYFT[i][j] - totalAbundanceYFT[i][j + 1];
+                        }
+                    }
+                    System.out.println("Yellowfin estimated");
+
+                    prevAbundYFT = fishState.getTotalAbundance(yft);
+
+                    Assertions.assertEquals(expectedBiomass.get(fishState.getStep()).get("YFT"), fishState.getTotalBiomass(yft), 1000000);
+
+
+                    System.out.println(fishState.getStep() + " " + fishState.getTotalBiomass(skj) / 1000);
+                    final double[][] totalAbundanceSKJ = fishState.getTotalAbundance(skj);
+                    for (int i = 0; i < totalAbundanceSKJ.length; i++) {
+                        for (int j = 0; j < totalAbundanceSKJ[0].length - 1; j++) {
+                            deaths[i][j] = prevAbundSKJ[i][j] - totalAbundanceSKJ[i][j + 1];
+                        }
+                    }
+                    System.out.println("Skipjack estimated");
+
+                    prevAbundSKJ = fishState.getTotalAbundance(skj);
+
+                    Assertions.assertEquals(expectedBiomass.get(fishState.getStep()).get("SKJ"), fishState.getTotalBiomass(skj), 1000000);*/
+            fishState.schedule.step(fishState);
+        } while (fishState.getYear() < 1);
+    }
+}
+
+
+