BrAPIServiceImpl.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.gringlobal.service.impl;

import java.util.List;
import java.util.stream.Collectors;

import org.apache.commons.lang3.StringUtils;
import org.gringlobal.custom.elasticsearch.SearchException;
import org.gringlobal.model.Accession;
import org.gringlobal.model.Crop;
import org.gringlobal.model.brapi.Germplasm;
import org.gringlobal.service.AccessionService;
import org.gringlobal.service.BrAPIService;
import org.gringlobal.service.CropService;
import org.gringlobal.service.filter.AccessionFilter;
import org.gringlobal.worker.AccessionMCPDConverter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageImpl;
import org.springframework.data.domain.Pageable;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;

/**
 * BrAPI v1 implementation
 */
@Service
@Transactional(readOnly = true)
public class BrAPIServiceImpl implements BrAPIService {

	@Autowired
	private AccessionService accessionService;

	@Autowired
	private CropService cropService;

	@Autowired
	private AccessionMCPDConverter accessionMCPDConverter;

	@Override
	public Page<String> getCrops(Pageable pageable) {
		Page<Crop> crops = cropService.listCrops(pageable);
		return new PageImpl<>(crops.getContent().stream().map(Crop::getName).collect(Collectors.toList()), pageable, crops.getTotalElements());
	}

	@Override
	public Germplasm getGermplasmById(long germplasmId) {
		return toGermplasm(accessionService.get(germplasmId));
	}

	@Override
	public Page<Germplasm> searchGermplasm(String germplasmName, String germplasmPUI, Long germplasmDbId, Pageable page) throws SearchException {
		AccessionFilter accessionFilter = new AccessionFilter();

		if (StringUtils.isNotBlank(germplasmPUI)) {
			accessionFilter.doi().add(germplasmPUI);
		}

		if (germplasmDbId != null) {
			accessionFilter.id().add(germplasmDbId);
		}

		if (StringUtils.isNotBlank(germplasmName)) {
			accessionFilter.accessionNumbers().add(germplasmName);
		}

		Page<Accession> accessions = accessionService.list(accessionFilter, page);
		return new PageImpl<>(accessions.getContent().stream().map(this::toGermplasm).collect(Collectors.toList()), page, accessions.getTotalElements());
	}

	@Override
	public Page<Germplasm> searchGermplasm(AccessionFilter filter, Pageable page) throws SearchException {
		Page<Accession> accessions = accessionService.list(filter, page);
		return new PageImpl<>(accessions.getContent().stream().map(this::toGermplasm).collect(Collectors.toList()), page, accessions.getTotalElements());
	}

	/**
	 * Convert Accession to Germplasm
	 */
	// TODO Add details
	private Germplasm toGermplasm(Accession accession) {
		var mcpd = accessionMCPDConverter.convert(accession);
		Germplasm g = new Germplasm();

		g.setId(Long.toString(accession.getId()));
		g.setGermplasmPUI(mcpd.puid);
		g.setAcceNumb(mcpd.acceNumb);
		g.setAcceName(mcpd.acceName);
		g.setDefaultDisplayName(StringUtils.defaultIfBlank(mcpd.acceName, mcpd.acceNumb));
		if (StringUtils.isNotBlank(mcpd.otherNumb)) {
			g.setSynonyms(List.of(mcpd.otherNumb.split(";")));
		}

		g.setInstCode(mcpd.instCode);
		g.setInstName(accession.getSite().getSiteLongName());

		g.setGenus(mcpd.genus);
		g.setSpecies(mcpd.species);
		g.setSpAuthor(mcpd.spAuthor);
		g.setSubtaxa(mcpd.subtaxa);
		g.setSubtAuthor(mcpd.subtAuthor);

		g.setAcqDate(mcpd.acqDate);
		g.setPedigree(mcpd.ancest);

		g.setCommonCropName(mcpd.cropName);
		g.setSampStat(mcpd.sampStat);

		g.setOrigCty(mcpd.origCty);
//		g.setStorage(mcpd.storage);

		return g;
	}
}