TaxonomyService.java

/*
 * Copyright 2020 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.server.service;

import java.io.Serializable;
import java.util.Collection;
import java.util.List;

import org.genesys.server.model.genesys.Taxonomy2;
import org.genesys.server.model.grin.TaxonomySpecies;
import org.genesys.server.service.filter.TaxonomyExtraFilter;
import org.genesys.server.service.filter.TaxonomyFilter;
import org.genesys.server.service.filter.TaxonomySpeciesFilter;
import org.genesys.server.exception.SearchException;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;

import com.fasterxml.jackson.annotation.JsonUnwrapped;

public interface TaxonomyService {

	List<String> autocompleteGenus(String term);

	List<String> autocompleteSpecies(String term, List<String> genus);

	List<String> autocompleteTaxonomy(String term);

	List<String> autocompleteSubtaxa(String term, List<String> genus, List<String> species);

	long getTaxonomy2Id(String genus);

	long getTaxonomy2Id(String genus, String species);

	long countTaxonomy2();

	Taxonomy2 get(Long id);

	Taxonomy2 get(String genus);

	List<Taxonomy2> list(TaxonomyFilter filter);

	Page<Taxonomy2Info> list(TaxonomyExtraFilter filter, Pageable page);

	Page<TaxonomySpecies> listSpecies(TaxonomySpeciesFilter filter, Pageable page) throws SearchException;

	Taxonomy2 setGrinSpecies(long taxonomy2Id, Long customGrinSpeciesId);

	List<String> getAllGenera();

	Taxonomy2 get(String genus, String species);

	Taxonomy2 find(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);

	Taxonomy2 internalEnsure(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) throws InterruptedException;

	List<Long> findByGenus(List<String> genus);

	void cleanupTaxonomies();

	Taxonomy2 ensureTaxonomy(Taxonomy2 source);

	List<Long> findTaxonomy2GenusId(List<String> genera);
	List<Long> findTaxonomy2SpeciesId(List<String> speciesNames);

	List<Long> findGrinGenusId(List<String> genera);
	List<Long> findGrinSpeciesId(List<String> speciesNames);

	public static class Taxonomy2Info implements Serializable {
		private static final long serialVersionUID = 2114693656081783236L;

		@JsonUnwrapped
		public Taxonomy2 taxonomy;
		public Long accessionCount;

		public static Taxonomy2Info from(Taxonomy2 taxonomy, Long accessionCount) {
			Taxonomy2Info taxonomy2Info = new Taxonomy2Info();
			taxonomy2Info.taxonomy = taxonomy;
			taxonomy2Info.accessionCount = accessionCount;
			return taxonomy2Info;
		}
	}

	List<Long> findTaxonomy2ByGrinGenus(List<String> genus);
	List<Long> findTaxonomy2ByCurrentGrinGenus(List<String> genus);

	List<Long> findTaxonomy2ByGrinSpecies(List<String> genusSpecies);
	List<Long> findTaxonomy2ByCurrentGrinSpecies(List<String> genusSpecies);

	List<Long> findTaxonomy2ByGrinNames(List<String> names);
	List<Long> findTaxonomy2ByCurrentGrinNames(List<String> names);

	List<Long> listTaxonomy2ByGrinId(Collection<Long> grinId);
	List<Long> listTaxonomy2ByCurrentGrinId(Collection<Long> grinId);

	/** Populate blank Taxonomy2.family using GRIN species.genus.family.name */
	void updateFamilyNames();

}