RetractedDoiServiceImpl.java

/*
 * Copyright 2026 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.impl;

import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import javax.persistence.EntityNotFoundException;

import org.genesys.server.model.filters.RetractedDOIFilter;
import org.genesys.server.model.genesys.Accession;
import org.genesys.server.model.impl.RetractedDOI;
import org.genesys.server.persistence.AccessionRepository;
import org.genesys.server.persistence.RetractedDoiRepository;
import org.genesys.server.service.RetractedDoiService;

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;

@Service
@Transactional(readOnly = true)
public class RetractedDoiServiceImpl extends FilteredCRUDService2Impl<RetractedDOI, RetractedDOIFilter, RetractedDoiRepository> implements RetractedDoiService {

	@Autowired
	private RetractedDoiRepository retractedDoiRepository;

	@Autowired
	private AccessionRepository accessionRepository;

	@Override
	@Transactional
	@PreAuthorize("hasRole('ADMINISTRATOR') || hasRole('RETRACT_DOI')")
	public List<RetractedDOI> retractDOI(List<RetractedDOI> retractedList) {
		List<RetractedDOI> retracted = new ArrayList<>(retractedList.size());
		for (RetractedDOI item : retractedList) {
			RetractedDOI existing = retractedDoiRepository.findByDoi((item.getDoi())).orElse(null);
			retracted.add(Objects.requireNonNullElseGet(existing, () -> retractedDoiRepository.save(item)));
		}
		// Clear matching DOI on accessions
		List<Accession> accessions = accessionRepository.findByDoiIn(retracted.stream().map(RetractedDOI::getDoi).collect(Collectors.toList()));
		accessions.forEach(accession -> accession.setDoi(null));
		accessionRepository.saveAllAndFlush(accessions);
		return retracted;
	}

	@Override
	public RetractedDOI get(String doi) {
		return retractedDoiRepository.findByDoi(doi).orElseThrow(() -> new EntityNotFoundException("Retracted DOI not found."));
	}

	@Override
	@PreAuthorize("hasRole('ADMINISTRATOR')")
	public RetractedDOI remove(RetractedDOI entity) {
		return super.remove(entity);
	}

	@Override
	public RetractedDOI create(RetractedDOI source) {
		throw new UnsupportedOperationException();
	}

	@Override
	public RetractedDOI createFast(RetractedDOI source) {
		throw new UnsupportedOperationException();
	}

	@Override
	public RetractedDOI update(RetractedDOI updated, RetractedDOI target) {
		throw new UnsupportedOperationException();
	}

	@Override
	public RetractedDOI updateFast(RetractedDOI updated, RetractedDOI target) {
		throw new UnsupportedOperationException();
	}
}