package net.sumaris.core.dao.data;
   
   /*-
    * #%L
    * SUMARiS:: Core
    * %%
    * Copyright (C) 2018 SUMARiS Consortium
    * %%
    * This program is free software: you can redistribute it and/or modify
   * it under the terms of the GNU General Public License as
   * published by the Free Software Foundation, either version 3 of the
   * License, or (at your option) any later version.
   * 
   * This program is distributed in the hope that it will be useful,
   * but WITHOUT ANY WARRANTY; without even the implied warranty of
   * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   * GNU General Public License for more details.
   * 
   * You should have received a copy of the GNU General Public
   * License along with this program.  If not, see
   * <http://www.gnu.org/licenses/gpl-3.0.html>.
   * #L%
   */
  
  import com.google.common.base.Preconditions;
  import net.sumaris.core.dao.administration.user.PersonDao;
  import net.sumaris.core.dao.referential.ReferentialDao;
  import net.sumaris.core.dao.referential.taxon.TaxonNameDao;
  import net.sumaris.core.model.administration.programStrategy.PmfmStrategy;
  import net.sumaris.core.model.data.Batch;
  import net.sumaris.core.model.data.Landing;
  import net.sumaris.core.model.data.Operation;
  import net.sumaris.core.model.data.Sample;
  import net.sumaris.core.model.referential.pmfm.Matrix;
  import net.sumaris.core.model.referential.pmfm.Unit;
  import net.sumaris.core.model.referential.taxon.TaxonGroup;
  import net.sumaris.core.model.referential.taxon.TaxonName;
  import net.sumaris.core.util.Beans;
  import net.sumaris.core.vo.administration.programStrategy.ProgramVO;
  import net.sumaris.core.vo.administration.user.DepartmentVO;
  import net.sumaris.core.vo.administration.user.PersonVO;
  import net.sumaris.core.vo.data.LandingVO;
  import net.sumaris.core.vo.data.OperationVO;
  import net.sumaris.core.vo.data.SampleVO;
  import net.sumaris.core.vo.referential.ReferentialVO;
  import org.apache.commons.collections4.CollectionUtils;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  import org.springframework.beans.factory.annotation.Autowired;
  import org.springframework.stereotype.Repository;
  
  import javax.annotation.PostConstruct;
  import javax.persistence.EntityManager;
  import javax.persistence.criteria.CriteriaBuilder;
  import javax.persistence.criteria.CriteriaQuery;
  import javax.persistence.criteria.ParameterExpression;
  import javax.persistence.criteria.Root;
  import java.sql.Timestamp;
  import java.util.List;
  import java.util.Objects;
  import java.util.stream.Collectors;
  import java.util.stream.Stream;
  
  @Repository("sampleDao")
  public class SampleDaoImpl extends BaseDataDaoImpl implements SampleDao {
  
      /** Logger. */
      private static final Logger log =
              LoggerFactory.getLogger(SampleDaoImpl.class);
  
      @Autowired
      private ReferentialDao referentialDao;
  
      @Autowired
      private TaxonNameDao taxonNameDao;
  
      @Autowired
      private PersonDao personDao;
  
      private int unitIdNone;
  
      @PostConstruct
      protected void init() {
          this.unitIdNone = config.getUnitIdNone();
      }
  
      @Override
      @SuppressWarnings("unchecked")
      public List<SampleVO> getAllByOperationId(int operationId) {
  
          CriteriaBuilder cb = getEntityManager().getCriteriaBuilder();
          CriteriaQuery<Sample> query = cb.createQuery(Sample.class);
          Root<Sample> root = query.from(Sample.class);
  
          query.select(root);
  
          ParameterExpression<Integer> tripIdParam = cb.parameter(Integer.class);
  
          query.where(cb.equal(root.get(Sample.Fields.OPERATION).get(Operation.Fields.ID), tripIdParam));
 
         // Sort by rank order
         query.orderBy(cb.asc(root.get(PmfmStrategy.Fields.RANK_ORDER)));
 
         return toSampleVOs(getEntityManager().createQuery(query)
                 .setParameter(tripIdParam, operationId).getResultList(), false);
     }
 
     @Override
     @SuppressWarnings("unchecked")
     public List<SampleVO> getAllByLandingId(int landingId) {
 
         CriteriaBuilder cb = getEntityManager().getCriteriaBuilder();
         CriteriaQuery<Sample> query = cb.createQuery(Sample.class);
         Root<Sample> root = query.from(Sample.class);
 
         query.select(root);
 
         ParameterExpression<Integer> idParam = cb.parameter(Integer.class);
 
         query.where(cb.equal(root.get(Sample.Fields.LANDING).get(Landing.Fields.ID), idParam));
 
         // Sort by rank order
         query.orderBy(cb.asc(root.get(PmfmStrategy.Fields.RANK_ORDER)));
 
         return toSampleVOs(getEntityManager().createQuery(query)
                 .setParameter(idParam, landingId).getResultList(), false);
     }
 
 
     @Override
     public SampleVO get(int id) {
         Sample entity = get(Sample.class, id);
         return toSampleVO(entity, false);
     }
 
     @Override
     public List<SampleVO> saveByOperationId(int operationId, List<SampleVO> sources) {
 
         // Load parent entity
         Operation parent = get(Operation.class, operationId);
         ProgramVOprogramStrategy/ProgramVO.html#ProgramVO">ProgramVO parentProgram = new ProgramVO();
         parentProgram.setId(parent.getTrip().getProgram().getId());
 
         // Remember existing entities
         final List<Integer> sourcesIdsToRemove = Beans.collectIds(Beans.getList(parent.getSamples()));
 
         // Save each entities
         List<SampleVO> result = sources.stream().map(source -> {
             source.setOperationId(operationId);
             source.setProgram(parentProgram);
             if (source.getId() != null) {
                 sourcesIdsToRemove.remove(source.getId());
             }
             return save(source);
         }).collect(Collectors.toList());
 
         // Remove unused entities
         if (CollectionUtils.isNotEmpty(sourcesIdsToRemove)) {
             sourcesIdsToRemove.forEach(this::delete);
         }
 
         // Remove parent (use only parentId)
         result.stream().forEach(sample -> {
             if (sample.getParent() != null) {
                 sample.setParentId(sample.getParent().getId());
                 sample.setParent(null);
             }
         });
 
         return result;
     }
 
     @Override
     public List<SampleVO> saveByLandingId(int landingId, List<SampleVO> sources) {
         // Load parent entity
         Landing parent = get(Landing.class, landingId);
         ProgramVOprogramStrategy/ProgramVO.html#ProgramVO">ProgramVO parentProgram = new ProgramVO();
         parentProgram.setId(parent.getProgram().getId());
 
         // Remember existing entities
         final List<Integer> sourcesIdsToRemove = Beans.collectIds(Beans.getList(parent.getSamples()));
 
         // Save each entities
         List<SampleVO> result = sources.stream().map(source -> {
             source.setLandingId(landingId);
             source.setProgram(parentProgram);
             if (source.getId() != null) {
                 sourcesIdsToRemove.remove(source.getId());
             }
             return save(source);
         }).collect(Collectors.toList());
 
         // Remove unused entities
         if (CollectionUtils.isNotEmpty(sourcesIdsToRemove)) {
             sourcesIdsToRemove.forEach(this::delete);
         }
 
         // Remove parent (use only parentId)
         result.stream().forEach(sample -> {
             if (sample.getParent() != null) {
                 sample.setParentId(sample.getParent().getId());
                 sample.setParent(null);
             }
         });
 
         return result;
     }
 
     @Override
     public SampleVOf="../../../../../net/sumaris/core/vo/data/SampleVO.html#SampleVO">SampleVO save(SampleVO source) {
         Preconditions.checkNotNull(source);
 
         EntityManager entityManager = getEntityManager();
         Sample entity = null;
         if (source.getId() != null) {
             entity = get(Sample.class, source.getId());
         }
         boolean isNew = (entity == null);
         if (isNew) {
             entity = new Sample();
         }
 
         if (!isNew) {
             // Check update date
             // TODO: check why SUMARiS app did not refresh sample's updateDate after a first save
             //checkUpdateDateForUpdate(source, entity);
 
             // Lock entityName
             //lockForUpdate(entity);
         }
 
         // Copy some fields from the trip
         copySomeFieldsFromParent(source);
 
         // VO -> Entity
         sampleVOToEntity(source, entity, true);
 
         // Update update_dt
         Timestamp newUpdateDate = getDatabaseCurrentTimestamp();
         entity.setUpdateDate(newUpdateDate);
 
         // Save entity
         if (isNew) {
             // Force creation date
             entity.setCreationDate(newUpdateDate);
             source.setCreationDate(newUpdateDate);
 
             entityManager.persist(entity);
             source.setId(entity.getId());
         } else {
             if (entity.getCreationDate() == null) {
                 log.warn("Recording a sample without creation date. Should never occur! Sample ID=" + entity.getId());
                 entity.setCreationDate(newUpdateDate);
                 source.setCreationDate(newUpdateDate);
             }
             entityManager.merge(entity);
         }
 
         source.setUpdateDate(newUpdateDate);
 
         // Update link to parent
         if (source.getParentId() == null && entity.getParent() != null) {
             source.setParentId(entity.getParent().getId());
         }
 
         entityManager.flush();
         entityManager.clear();
 
         return source;
     }
 
     @Override
     public void delete(int id) {
 
         log.debug(String.format("Deleting sample {id=%s}...", id));
         delete(Sample.class, id);
     }
 
     @Override
     public SampleVO toSampleVO(Sample source) {
         return toSampleVO(source, true);
     }
 
 
     /* -- protected methods -- */
 
     protected SampleVO toSampleVO(Sample source, boolean allFields) {
 
         if (source == null) return null;
 
         SampleVOmpleVO.html#SampleVO">SampleVO target = new SampleVO();
 
         Beans.copyProperties(source, target);
 
         // Matrix
         ReferentialVO matrix = referentialDao.toReferentialVO(source.getMatrix());
         target.setMatrix(matrix);
 
         // Size Unit
         if (source.getSizeUnit() != null && source.getSizeUnit().getId().intValue() != unitIdNone) {
             target.setSizeUnit(source.getSizeUnit().getLabel());
         }
 
         // Taxon group
         if (source.getTaxonGroup() != null) {
             ReferentialVO taxonGroup = referentialDao.toReferentialVO(source.getTaxonGroup());
             target.setTaxonGroup(taxonGroup);
         }
 
         // Taxon name (from reference)
         if (source.getReferenceTaxon() != null) {
             ReferentialVO taxonName = taxonNameDao.getTaxonNameReferent(source.getReferenceTaxon().getId());
             target.setTaxonName(taxonName);
         }
 
         // Parent sample
         if (source.getParent() != null) {
             target.setParentId(source.getParent().getId());
         }
 
         // Operation
         if (source.getOperation() != null) {
             target.setOperationId(source.getOperation().getId());
         }
         // Batch
         if (source.getBatch() != null) {
             target.setBatchId(source.getBatch().getId());
         }
 
         // If full export
         if (allFields) {
             // Recorder department
             DepartmentVO recorderDepartment = referentialDao.toTypedVO(source.getRecorderDepartment(), DepartmentVO.class).orElse(null);
             target.setRecorderDepartment(recorderDepartment);
 
             // Recorder person
             if (source.getRecorderPerson() != null) {
                 PersonVO recorderPerson = personDao.toPersonVO(source.getRecorderPerson());
                 target.setRecorderPerson(recorderPerson);
             }
         }
 
         return target;
     }
 
     protected void copySomeFieldsFromParent(SampleVO target) {
         OperationVO operation = target.getOperation();
         if (operation != null) {
             target.setRecorderDepartment(operation.getRecorderDepartment());
             return;
         }
         LandingVO landing = target.getLanding();
         if (landing != null) {
             target.setRecorderDepartment(landing.getRecorderDepartment());
             return;
         }
     }
 
     protected List<SampleVO> toSampleVOs(List<Sample> source, boolean allFields) {
         return this.toSampleVOs(source.stream(), allFields);
     }
 
     protected List<SampleVO> toSampleVOs(Stream<Sample> source, boolean allFields) {
         return source.map(s -> this.toSampleVO(s, allFields))
                 .filter(Objects::nonNull)
                 .collect(Collectors.toList());
     }
 
     protected void sampleVOToEntity(SampleVO source, Sample target, boolean copyIfNull) {
 
         copyRootDataProperties(source, target, copyIfNull);
 
         // Matrix
         if (copyIfNull || source.getMatrix() != null) {
             if (source.getMatrix() == null || source.getMatrix().getId() == null) {
                 target.setMatrix(null);
             }
             else {
                 target.setMatrix(load(Matrix.class, source.getMatrix().getId()));
             }
         }
 
         // Size Unit
         if (copyIfNull || source.getSizeUnit() != null) {
             if (source.getSizeUnit() == null) {
                 target.setSizeUnit(null);
             }
             else {
                 ReferentialVO unit = referentialDao.findByUniqueLabel(Unit.class.getSimpleName(), source.getSizeUnit());
                 Preconditions.checkNotNull(unit, String.format("Invalid 'sample.sizeUnit': unit symbol '%s' not exists", source.getSizeUnit()));
                 target.setSizeUnit(load(Unit.class, unit.getId()));
             }
         }
 
         // Taxon group
         if (copyIfNull || source.getTaxonGroup() != null) {
             if (source.getTaxonGroup() == null || source.getTaxonGroup().getId() == null) {
                 target.setTaxonGroup(null);
             }
             else {
                 target.setTaxonGroup(load(TaxonGroup.class, source.getTaxonGroup().getId()));
             }
         }
 
         // Reference taxon (from taxon name)
         if (copyIfNull || source.getTaxonName() != null) {
             if (source.getTaxonName() == null || source.getTaxonName().getId() == null) {
                 target.setReferenceTaxon(null);
             }
             else {
                 // Get the taxon name, then set reference taxon
                 TaxonName taxonname = get(TaxonName.class, source.getTaxonName().getId());
                 target.setReferenceTaxon(taxonname.getReferenceTaxon());
             }
         }
 
         Integer parentId = source.getParent() != null ? source.getParent().getId() : source.getParentId();
         Integer opeId = source.getOperationId() != null ? source.getOperationId() : (source.getOperation() != null ? source.getOperation().getId() : null);
         Integer landingId = source.getLandingId() != null ? source.getLandingId() : (source.getLanding() != null ? source.getLanding().getId() : null);
 
         // Parent sample
         if (copyIfNull || (parentId != null)) {
             if (parentId == null) {
                 target.setParent(null);
             }
             else {
                 Sample parent = load(Sample.class, parentId);
                 target.setParent(parent);
 
                 // Force operation from parent's operation
                 opeId = parent.getOperation().getId();
             }
         }
 
         // Operation
         if (copyIfNull || (opeId != null)) {
             if (opeId == null) {
                 target.setOperation(null);
             } else {
                 target.setOperation(load(Operation.class, opeId));
             }
         }
 
         // Landing
         if (copyIfNull || (landingId != null)) {
             if (landingId == null) {
                 target.setLanding(null);
             } else {
                 target.setLanding(load(Landing.class, landingId));
             }
         }
 
         // Batch
         Integer batchId = source.getBatchId() != null ? source.getBatchId() : (source.getBatch() != null ? source.getBatch().getId() : null);
         if (copyIfNull || (batchId != null)) {
             if (batchId == null) {
                 target.setBatch(null);
             }
             else {
                 target.setBatch(load(Batch.class, batchId));
             }
         }
     }
 }