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));
}
}