Updates for taxonomy-tools compatibility

src/main/java/org/genesys/taxonomy/checker/web/config/ApplicationConfig.java

@@ -28,11 +28,11 @@ import org.genesys.geotools.service.CountryOfOriginService;
 import org.genesys.geotools.service.LandOrSeaService;
 import org.genesys.geotools.service.impl.CountryOfOriginServiceImpl;
 import org.genesys.geotools.service.impl.LandOrSeaServiceImpl;
+import org.genesys.taxonomy.checker.CachingInMemoryTaxonomyDatabase;
 import org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase;
 import org.genesys.taxonomy.checker.TaxonomyChecker;
 import org.genesys.taxonomy.checker.TaxonomyException;
 import org.genesys.taxonomy.checker.web.service.ProcessService;
-import org.genesys.taxonomy.checker.web.service.impl.CachingInMemoryTaxonomyDatabase;
 import org.genesys.taxonomy.checker.web.service.impl.CountryProcessServiceImpl;
 import org.genesys.taxonomy.checker.web.service.impl.LandOrSeaProcessServiceImpl;
 import org.genesys.taxonomy.checker.web.service.impl.ProcessServiceImpl;

src/main/java/org/genesys/taxonomy/checker/web/service/impl/CachingInMemoryTaxonomyDatabase.java

-/*
- * Copyright 2017 Global Crop Diversity Trust
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.genesys.taxonomy.checker.web.service.impl;
-
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-
-import org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase;
-import org.genesys.taxonomy.gringlobal.model.SpeciesRow;
-
-import com.google.common.cache.Cache;
-import com.google.common.cache.CacheBuilder;
-
-/**
- * Guava cache supported in-memory taxonomy database.
- */
-public class CachingInMemoryTaxonomyDatabase extends InMemoryTaxonomyDatabase {
-	// private final static Logger LOG =
-	// LoggerFactory.getLogger(CachingInMemoryTaxonomyDatabase.class);
-
-	/** The cache genus species. */
-	private final Cache<String, List<SpeciesRow>> cacheGenusSpecies = CacheBuilder.newBuilder().maximumSize(100).build();
-
-	/** The cache genus suggestions. */
-	private final Cache<String, List<String>> cacheGenusSuggestions = CacheBuilder.newBuilder().maximumSize(100).build();
-
-	/** The cache species suggestions. */
-	private final Cache<String, List<String>> cacheSpeciesSuggestions = CacheBuilder.newBuilder().maximumSize(100).build();
-
-	/**
-	 * Gets the all genus species.
-	 *
-	 * @param genus the genus
-	 * @return the all genus species
-	 */
-	/*
-	 * (non-Javadoc)
-	 * @see
-	 * org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase#getAllGenusSpecies(java
-	 * .lang.String)
-	 */
-	@Override
-	protected List<SpeciesRow> getAllGenusSpecies(final String genus) {
-		try {
-			return cacheGenusSpecies.get(genus, () -> CachingInMemoryTaxonomyDatabase.super.getAllGenusSpecies(genus));
-		} catch (final ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/**
-	 * Find similar genus.
-	 *
-	 * @param genus the genus
-	 * @param maxSize the max size
-	 * @return the list
-	 */
-	/*
-	 * (non-Javadoc)
-	 * @see
-	 * org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase#findSimilarGenus(java.
-	 * lang.String, int)
-	 */
-	@Override
-	public List<String> findSimilarGenus(final String genus, final int maxSize) {
-		try {
-			return cacheGenusSuggestions.get(genus + "-" + maxSize, () -> CachingInMemoryTaxonomyDatabase.super.findSimilarGenus(genus, maxSize));
-		} catch (final ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/**
-	 * Find similar species.
-	 *
-	 * @param genus the genus
-	 * @param species the species
-	 * @param maxSize the max size
-	 * @return the list
-	 */
-	/*
-	 * (non-Javadoc)
-	 * @see
-	 * org.genesys.taxonomy.checker.InMemoryTaxonomyDatabase#findSimilarSpecies(java
-	 * .lang.String, java.lang.String, int)
-	 */
-	@Override
-	public List<String> findSimilarSpecies(final String genus, final String species, final int maxSize) {
-		try {
-			return cacheSpeciesSuggestions.get(genus + "-" + species + "-" + maxSize, () -> CachingInMemoryTaxonomyDatabase.super.findSimilarSpecies(genus, species, maxSize));
-		} catch (final ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-}

src/main/java/org/genesys/taxonomy/checker/web/service/impl/TaxonomyProcessServiceImpl.java

@@ -40,6 +40,7 @@ import org.genesys.taxonomy.checker.web.service.ProcessService;
 import org.genesys.taxonomy.checker.web.util.ApplicationUtils;
 import org.genesys.taxonomy.gringlobal.component.CabReader;
 import org.genesys.taxonomy.gringlobal.model.GenusRow;
+import org.genesys.taxonomy.gringlobal.model.IGrinSpecies;
 import org.genesys.taxonomy.gringlobal.model.SpeciesRow;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -326,14 +327,14 @@ public class TaxonomyProcessServiceImpl implements ProcessService {
 				}
 
 				if (outputHeaders.indexOf(ApplicationUtils.HEADER_GRINTAX_SPECIESID) >= 0) {
-					final List<SpeciesRow> speciesRows = taxonomyDatabase.findSpeciesRow(genus, species, StringUtils.defaultIfBlank(subtaxa, null));
+					final List<IGrinSpecies> speciesRows = taxonomyDatabase.findSpeciesRow(genus, species, StringUtils.defaultIfBlank(subtaxa, null));
 					if (speciesRows.size() == 1) {
-						final SpeciesRow speciesRow = speciesRows.get(0);
+						final IGrinSpecies speciesRow = speciesRows.get(0);
 						outputLine[outputHeaders.indexOf(ApplicationUtils.HEADER_GRINTAX_SPECIESID)] = speciesRow.getSpeciesId().toString();
 						outputLine[outputHeaders.indexOf(ApplicationUtils.HEADER_GRINTAX_SPECIESCURRENT)] = Boolean.toString(speciesRow.isCurrent());
 						if (!speciesRow.isCurrent() && toCurrentTaxa) {
 							LOG.debug("{} is not current", speciesRow);
-							final SpeciesRow currentSpecies = taxonomyDatabase.getSpeciesRow(speciesRow.getCurrentTaxonomySpeciesId());
+							final IGrinSpecies currentSpecies = taxonomyDatabase.getSpeciesRow(speciesRow.getCurrentTaxonomySpeciesId());
 							final String currentGenus = taxonomyDatabase.getGenus(currentSpecies.getGenusId());
 							// LOG.warn("Result: {}", Arrays.toString(outputLine));
 							updateOutputColumn(outputLine, outputHeaders.indexOf(ApplicationUtils.HEADER_GENUS_CHECK), currentGenus, genus, ApplicationUtils.CURRENT_SUFFIX);