BrAPIv2FacadeImpl.java

/*
 * Copyright 2023 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.brapi.v2.impl;

import java.util.Arrays;
import java.util.Set;

import org.apache.commons.lang3.StringUtils;
import org.genesys.blocks.model.filters.StringFilter;
import org.gringlobal.brapi.v2.BrAPIv2Facade;
import org.gringlobal.brapi.v2.BrAPIv2Mapper;
import org.gringlobal.custom.elasticsearch.SearchException;
import org.gringlobal.model.Crop;
import org.gringlobal.model.community.CommunityCodeValues;
import org.gringlobal.service.AccessionService;
import org.gringlobal.service.CodeValueService;
import org.gringlobal.service.CropService;
import org.gringlobal.service.CropTraitService;
import org.gringlobal.service.filter.AccessionFilter;
import org.gringlobal.service.filter.CodeValueFilter;
import org.gringlobal.service.filter.CropTraitFilter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
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;

import uk.ac.hutton.ics.brapi.resource.germplasm.attribute.Trait;
import uk.ac.hutton.ics.brapi.resource.germplasm.germplasm.Germplasm;
import uk.ac.hutton.ics.brapi.resource.germplasm.germplasm.Mcpd;
import uk.ac.hutton.ics.brapi.resource.phenotyping.observation.ObservationVariable;

/**
 * Implementation to get Traits information
 */
@Service
public class BrAPIv2FacadeImpl implements BrAPIv2Facade {

//	private static final org.slf4j.Logger LOG = org.slf4j.LoggerFactory.getLogger(BrAPIv2FacadeImpl.class);

	@Autowired
	@Lazy
	private CodeValueService codeValueService;

	@Autowired
	@Lazy
	private CropTraitService cropTraitService;

	@Autowired
	@Lazy
	private CropService cropService;

	@Autowired
	@Lazy
	private AccessionService accessionService;

	@Autowired
	@Lazy
	private BrAPIv2Mapper brAPIv2Mapper;


	@Override
	public Page<String> getCommonCropNames(Pageable page) {
		return cropService.list(page).map(Crop::getName);
	}

	@Override
	public Page<String> getStudyTypes(Pageable page) throws Exception {
		var filter = new CodeValueFilter()
			.groupName(new StringFilter().eq(Set.of(CommunityCodeValues.METHOD_STUDY_TYPE)));
		return BrAPIv2Mapper.map(codeValueService.listFiltered(filter, page), tcv -> StringUtils.defaultIfBlank(tcv.title, tcv.entity.getValue()));
	}

	@Override
	@Transactional(readOnly = true)
	public Page<Germplasm> listAccessions(AccessionFilter filter, Pageable page) throws SearchException {
		return BrAPIv2Mapper.map(accessionService.list(filter, page), brAPIv2Mapper::map);
	}

	@Override
	@Transactional(readOnly = true)
	public Germplasm getAccession(long germplasmDbId) {
		return brAPIv2Mapper.map(accessionService.get(germplasmDbId));
	}

	@Override
	@Transactional(readOnly = true)
	public Mcpd getAccessionMcpd(long germplasmDbId) {
		return brAPIv2Mapper.mapMcpd(accessionService.get(germplasmDbId));
	}

	@Override
	@Transactional
	public Page<Germplasm> createAccessions(Germplasm... accessions) throws SearchException {
		var created = accessionService.create(BrAPIv2Mapper.map(Arrays.asList(accessions), brAPIv2Mapper::map)).success;
		return new PageImpl<>(created).map(brAPIv2Mapper::map);
	}

	@Override
	@Transactional
	public Germplasm updateAccession(long germplasmDbId, Germplasm accession) throws Exception {
		var target = accessionService.get(germplasmDbId);
		return brAPIv2Mapper.map(accessionService.update(brAPIv2Mapper.map(accession), target));
	}

	/*
	 * Traits
	 */

	@Override
	@Transactional(readOnly = true)
	public Page<Trait> listTraits(CropTraitFilter filter, Pageable page) throws SearchException {
		return BrAPIv2Mapper.map(cropTraitService.listFiltered(filter, page), brAPIv2Mapper::map);
	}

	@Override
	@Transactional(readOnly = true)
	public Trait getTrait(long traitDbId) {
		return brAPIv2Mapper.map(cropTraitService.loadTranslated(traitDbId));
	}

	@Override
	@Transactional
	public Trait updateTrait(long traitDbId, Trait trait) {
		var target = cropTraitService.get(traitDbId);
		return brAPIv2Mapper.map(cropTraitService.update(brAPIv2Mapper.map(trait), target));
	}

	@Override
	@Transactional
	public Page<Trait> createTraits(Trait... traits) {
		var created = cropTraitService.create(BrAPIv2Mapper.map(Arrays.asList(traits), brAPIv2Mapper::map)).success;
		return new PageImpl<>(created).map(brAPIv2Mapper::map);
	}

	/*
	 * Observation Variables
	 */

	@Override
	@Transactional(readOnly = true)
	public Page<ObservationVariable> listObservationVariables(CropTraitFilter filter, Pageable page) throws Exception {
		return BrAPIv2Mapper.map(cropTraitService.listFiltered(filter, page), brAPIv2Mapper::mapVariable);
	}

	@Override
	@Transactional(readOnly = true)
	public ObservationVariable getObservationVariable(long observationVariableDbId) {
		return brAPIv2Mapper.mapVariable(cropTraitService.loadTranslated(observationVariableDbId));
	}

	@Override
	@Transactional
	public Page<ObservationVariable> createObservationVariables(ObservationVariable... variables) {
		var created = cropTraitService.create(BrAPIv2Mapper.map(Arrays.asList(variables), brAPIv2Mapper::map)).success;
		return new PageImpl<>(created).map(brAPIv2Mapper::mapVariable);
	}

	@Override
	@Transactional
	public ObservationVariable updateObservationVariable(long observationVariableDbId, ObservationVariable variable) {
		var target = cropTraitService.get(observationVariableDbId);
		return brAPIv2Mapper.mapVariable(cropTraitService.update(brAPIv2Mapper.map(variable), target));
	}


}