org.molgenis.semanticmapper.service.impl.MappingServiceImpl Maven / Gradle / Ivy

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package org.molgenis.semanticmapper.service.impl;

import static com.google.common.collect.Maps.newHashMap;
import static java.lang.Boolean.TRUE;
import static java.lang.String.format;
import static java.util.Objects.requireNonNull;
import static java.util.stream.Collectors.toList;
import static org.molgenis.data.EntityManager.CreationMode.POPULATE;
import static org.molgenis.data.meta.model.EntityType.AttributeCopyMode.DEEP_COPY_ATTRS;
import static org.molgenis.data.meta.model.PackageMetadata.PACKAGE;
import static org.molgenis.data.util.EntityTypeUtils.hasSelfReferences;
import static org.molgenis.data.util.EntityTypeUtils.isReferenceType;
import static org.molgenis.semanticmapper.meta.MappingProjectMetadata.MAPPING_PROJECT;
import static org.molgenis.semanticmapper.meta.MappingProjectMetadata.NAME;

import java.util.List;
import java.util.Map;
import java.util.concurrent.atomic.AtomicLong;
import java.util.function.Predicate;
import java.util.stream.Stream;
import org.molgenis.data.DataService;
import org.molgenis.data.Entity;
import org.molgenis.data.EntityManager;
import org.molgenis.data.MolgenisDataException;
import org.molgenis.data.Repository;
import org.molgenis.data.UnknownEntityException;
import org.molgenis.data.UnknownEntityTypeException;
import org.molgenis.data.meta.AttributeType;
import org.molgenis.data.meta.model.Attribute;
import org.molgenis.data.meta.model.AttributeFactory;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.data.meta.model.Package;
import org.molgenis.data.security.permission.PermissionSystemService;
import org.molgenis.data.support.QueryImpl;
import org.molgenis.jobs.Progress;
import org.molgenis.semanticmapper.mapping.model.AttributeMapping;
import org.molgenis.semanticmapper.mapping.model.EntityMapping;
import org.molgenis.semanticmapper.mapping.model.MappingProject;
import org.molgenis.semanticmapper.mapping.model.MappingTarget;
import org.molgenis.semanticmapper.repository.MappingProjectRepository;
import org.molgenis.semanticmapper.service.AlgorithmService;
import org.molgenis.semanticmapper.service.MappingService;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.transaction.annotation.Transactional;

@PreAuthorize("hasAnyRole('ROLE_SU')")
public class MappingServiceImpl implements MappingService {
  public static final int MAPPING_BATCH_SIZE = 1000;

  static final String SOURCE = "source";

  private final DataService dataService;
  private final AlgorithmService algorithmService;
  private final MappingProjectRepository mappingProjectRepository;
  private final PermissionSystemService permissionSystemService;
  private final AttributeFactory attrMetaFactory;
  private final EntityManager entityManager;

  public MappingServiceImpl(
      DataService dataService,
      AlgorithmService algorithmService,
      MappingProjectRepository mappingProjectRepository,
      PermissionSystemService permissionSystemService,
      AttributeFactory attrMetaFactory,
      EntityManager entityManager) {
    this.dataService = requireNonNull(dataService);
    this.algorithmService = requireNonNull(algorithmService);
    this.mappingProjectRepository = requireNonNull(mappingProjectRepository);
    this.permissionSystemService = requireNonNull(permissionSystemService);
    this.attrMetaFactory = requireNonNull(attrMetaFactory);
    this.entityManager = requireNonNull(entityManager);
  }

  @Override
  @Transactional
  public MappingProject addMappingProject(String projectName, String target, int depth) {
    MappingProject mappingProject = new MappingProject(projectName, depth);
    mappingProject.addTarget(dataService.getEntityType(target));
    mappingProjectRepository.add(mappingProject);
    return mappingProject;
  }

  @Override
  @Transactional
  public void deleteMappingProject(String mappingProjectId) {
    mappingProjectRepository.delete(mappingProjectId);
  }

  @Override
  @Transactional
  public MappingProject cloneMappingProject(String mappingProjectId) {
    MappingProject mappingProject = mappingProjectRepository.getMappingProject(mappingProjectId);
    if (mappingProject == null) {
      throw new UnknownEntityException(MAPPING_PROJECT, mappingProjectId);
    }
    String mappingProjectName = mappingProject.getName();

    // determine cloned mapping project name (use Windows 7 naming strategy):
    String clonedMappingProjectName;
    for (int i = 1; ; ++i) {
      if (i == 1) {
        clonedMappingProjectName = mappingProjectName + " - Copy";
      } else {
        clonedMappingProjectName = mappingProjectName + " - Copy (" + i + ")";
      }

      if (mappingProjectRepository
          .getMappingProjects(new QueryImpl<>().eq(NAME, clonedMappingProjectName))
          .isEmpty()) {
        break;
      }
    }

    return cloneMappingProject(mappingProject, clonedMappingProjectName);
  }

  @Override
  @Transactional
  public MappingProject cloneMappingProject(
      String mappingProjectId, String clonedMappingProjectName) {
    MappingProject mappingProject = mappingProjectRepository.getMappingProject(mappingProjectId);
    if (mappingProject == null) {
      throw new UnknownEntityException(MAPPING_PROJECT, mappingProjectId);
    }

    return cloneMappingProject(mappingProject, clonedMappingProjectName);
  }

  private MappingProject cloneMappingProject(
      MappingProject mappingProject, String clonedMappingProjectName) {
    mappingProject.removeIdentifiers();
    mappingProject.setName(clonedMappingProjectName);
    mappingProjectRepository.add(mappingProject);
    return mappingProject;
  }

  @Override
  public List getAllMappingProjects() {
    return mappingProjectRepository.getAllMappingProjects();
  }

  @Override
  @Transactional
  public void updateMappingProject(MappingProject mappingProject) {
    mappingProjectRepository.update(mappingProject);
  }

  @Override
  public MappingProject getMappingProject(String identifier) {
    return mappingProjectRepository.getMappingProject(identifier);
  }

  @Override
  @Transactional
  public long applyMappings(
      String mappingProjectId,
      String entityTypeId,
      Boolean addSourceAttribute,
      String packageId,
      String label,
      Progress progress) {
    MappingProject mappingProject = getMappingProject(mappingProjectId);
    MappingTarget mappingTarget = mappingProject.getMappingTargets().get(0);
    progress.setProgressMax(calculateMaxProgress(mappingTarget));

    progress.progress(0, format("Checking target repository [%s]...", entityTypeId));
    EntityType targetMetadata =
        createTargetMetadata(mappingTarget, entityTypeId, packageId, label, addSourceAttribute);
    Repository targetRepo = getTargetRepository(entityTypeId, targetMetadata);
    return applyMappingsInternal(mappingTarget, targetRepo, progress, mappingProject.getDepth());
  }

  /** Package-private for testability */
  EntityType createTargetMetadata(
      MappingTarget mappingTarget,
      String entityTypeId,
      String packageId,
      String label,
      Boolean addSourceAttribute) {
    EntityType targetMetadata =
        EntityType.newInstance(mappingTarget.getTarget(), DEEP_COPY_ATTRS, attrMetaFactory);
    targetMetadata.setId(entityTypeId);

    if (label != null) {
      targetMetadata.setLabel(label);
    } else {
      targetMetadata.setLabel(entityTypeId);
    }

    if (TRUE.equals(addSourceAttribute)) {
      targetMetadata.addAttribute(attrMetaFactory.create().setName(SOURCE));
    }

    if (dataService.hasRepository(entityTypeId)) {
      EntityType entityType =
          dataService
              .getMeta()
              .getEntityType(entityTypeId)
              .orElseThrow(() -> new UnknownEntityTypeException(entityTypeId));
      targetMetadata.setPackage(entityType.getPackage());
    } else if (packageId != null) {
      Package aPackage =
          dataService
              .getMeta()
              .getPackage(packageId)
              .orElseThrow(() -> new UnknownEntityException(PACKAGE, packageId));
      targetMetadata.setPackage(aPackage);
    } else {
      throw new MolgenisDataException("Package can't be null");
    }

    return targetMetadata;
  }

  private Repository getTargetRepository(String entityTypeId, EntityType targetMetadata) {
    Repository targetRepo;
    if (!dataService.hasRepository(entityTypeId)) {
      targetRepo = addTargetEntityType(targetMetadata);
    } else {
      targetRepo = dataService.getRepository(entityTypeId);
      compareTargetMetadatas(targetRepo.getEntityType(), targetMetadata);
    }
    return targetRepo;
  }

  private Repository addTargetEntityType(EntityType targetMetadata) {
    Repository targetRepo = dataService.getMeta().createRepository(targetMetadata);
    permissionSystemService.giveUserWriteMetaPermissions(targetMetadata);
    return targetRepo;
  }

  private long applyMappingsInternal(
      MappingTarget mappingTarget, Repository targetRepo, Progress progress, int depth) {
    progress.status("Applying mappings to repository [" + targetRepo.getEntityType().getId() + "]");
    long result = applyMappingsToRepositories(mappingTarget, targetRepo, progress, depth);
    if (hasSelfReferences(targetRepo.getEntityType())) {
      progress.status(
          "Self reference found, applying the mapping for a second time to set references");
      applyMappingsToRepositories(mappingTarget, targetRepo, progress, depth);
    }
    progress.status(
        "Done applying mappings to repository [" + targetRepo.getEntityType().getId() + "]");
    return result;
  }

  /** Public for testability */
  public Stream getCompatibleEntityTypes(EntityType target) {
    return dataService
        .getMeta()
        .getEntityTypes()
        .filter(candidate -> !candidate.isAbstract())
        .filter(isCompatible(target));
  }

  private Predicate isCompatible(EntityType target) {
    return candidate -> {
      try {
        compareTargetMetadatas(candidate, target);
        return true;
      } catch (MolgenisDataException incompatible) {
        return false;
      }
    };
  }

  /**
   * Compares the attributes between the target repository and the mapping target. Applied Rules: -
   * The mapping target can not contain attributes which are not in the target repository - The
   * attributes of the mapping target with the same name as attributes in the target repository
   * should have the same type - If there are reference attributes, the name of the reference entity
   * should be the same in both the target repository as in the mapping target
   *
   * @param targetRepositoryEntityType the target repository EntityType to check
   * @param mappingTargetEntityType the mapping target EntityType to check
   * @throws MolgenisDataException if the types are not compatible
   */
  private void compareTargetMetadatas(
      EntityType targetRepositoryEntityType, EntityType mappingTargetEntityType) {
    Map targetRepositoryAttributeMap = newHashMap();
    targetRepositoryEntityType
        .getAtomicAttributes()
        .forEach(attribute -> targetRepositoryAttributeMap.put(attribute.getName(), attribute));

    for (Attribute mappingTargetAttribute : mappingTargetEntityType.getAtomicAttributes()) {
      String mappingTargetAttributeName = mappingTargetAttribute.getName();
      Attribute targetRepositoryAttribute =
          targetRepositoryAttributeMap.get(mappingTargetAttributeName);
      if (targetRepositoryAttribute == null) {
        throw new MolgenisDataException(
            format(
                "Target repository does not contain the following attribute: %s",
                mappingTargetAttributeName));
      }

      AttributeType targetRepositoryAttributeType = targetRepositoryAttribute.getDataType();
      AttributeType mappingTargetAttributeType = mappingTargetAttribute.getDataType();
      if (!mappingTargetAttributeType.equals(targetRepositoryAttributeType)) {
        throw new MolgenisDataException(
            format(
                "attribute %s in the mapping target is type %s while attribute %s in the target repository is type %s. Please make sure the types are the same",
                mappingTargetAttributeName,
                mappingTargetAttributeType,
                targetRepositoryAttribute.getName(),
                targetRepositoryAttributeType));
      }

      if (isReferenceType(mappingTargetAttribute)) {
        String mappingTargetRefEntityName = mappingTargetAttribute.getRefEntity().getId();
        String targetRepositoryRefEntityName = targetRepositoryAttribute.getRefEntity().getId();
        if (!mappingTargetRefEntityName.equals(targetRepositoryRefEntityName)) {
          throw new MolgenisDataException(
              format(
                  "In the mapping target, attribute %s of type %s has reference entity %s while in the target repository attribute %s of type %s has reference entity %s. "
                      + "Please make sure the reference entities of your mapping target are pointing towards the same reference entities as your target repository",
                  mappingTargetAttributeName,
                  mappingTargetAttributeType,
                  mappingTargetRefEntityName,
                  targetRepositoryAttribute.getName(),
                  targetRepositoryAttributeType,
                  targetRepositoryRefEntityName));
        }
      }
    }
  }

  private long applyMappingsToRepositories(
      MappingTarget mappingTarget, Repository targetRepo, Progress progress, int depth) {
    return mappingTarget.getEntityMappings().stream()
        .mapToLong(sourceMapping -> applyMappingToRepo(sourceMapping, targetRepo, progress, depth))
        .sum();
  }

  /** Package-private for testability */
  long applyMappingToRepo(
      EntityMapping sourceMapping, Repository targetRepo, Progress progress, int depth) {
    progress.status(format("Mapping source [%s]...", sourceMapping.getLabel()));
    AtomicLong counter = new AtomicLong();

    boolean canAdd = targetRepo.count() == 0;
    dataService
        .getRepository(sourceMapping.getName())
        .forEachBatched(
            entities ->
                processBatch(sourceMapping, targetRepo, progress, counter, canAdd, entities, depth),
            MAPPING_BATCH_SIZE);

    progress.status(format("Mapped %s [%s] entities.", counter, sourceMapping.getLabel()));
    return counter.get();
  }

  private void processBatch(
      EntityMapping sourceMapping,
      Repository targetRepo,
      Progress progress,
      AtomicLong counter,
      boolean canAdd,
      List entities,
      int depth) {
    List mappedEntities =
        mapEntities(sourceMapping, targetRepo.getEntityType(), entities, depth);
    if (canAdd) {
      targetRepo.add(mappedEntities.stream());
    } else {
      targetRepo.upsertBatch(mappedEntities);
    }
    progress.increment(1);
    counter.addAndGet(entities.size());
  }

  private List mapEntities(
      EntityMapping sourceMapping, EntityType targetMetaData, List entities, int depth) {
    return entities.stream()
        .map(
            sourceEntity ->
                applyMappingToEntity(sourceMapping, sourceEntity, targetMetaData, depth))
        .collect(toList());
  }

  /** Package-private for testablility */
  Entity applyMappingToEntity(
      EntityMapping sourceMapping, Entity sourceEntity, EntityType targetMetaData, int depth) {
    Entity target = entityManager.create(targetMetaData, POPULATE);

    if (targetMetaData.getAttribute(SOURCE) != null) {
      target.set(SOURCE, sourceMapping.getName());
    }

    sourceMapping
        .getAttributeMappings()
        .forEach(
            attributeMapping ->
                applyMappingToAttribute(
                    attributeMapping,
                    sourceEntity,
                    target,
                    sourceMapping.getSourceEntityType(),
                    depth));
    return target;
  }

  private void applyMappingToAttribute(
      AttributeMapping attributeMapping,
      Entity sourceEntity,
      Entity target,
      EntityType entityType,
      int depth) {
    String targetAttributeName = attributeMapping.getTargetAttribute().getName();
    Object typedValue = algorithmService.apply(attributeMapping, sourceEntity, entityType, depth);
    target.set(targetAttributeName, typedValue);
  }

  /** Package-private for testablility */
  int calculateMaxProgress(MappingTarget mappingTarget) {
    int batches = mappingTarget.getEntityMappings().stream().mapToInt(this::countBatches).sum();
    if (mappingTarget.hasSelfReferences()) {
      batches *= 2;
    }
    return batches;
  }

  private int countBatches(EntityMapping entityMapping) {
    long sourceRows = dataService.count(entityMapping.getSourceEntityType().getId());

    long batches = sourceRows / MAPPING_BATCH_SIZE;
    long remainder = sourceRows % MAPPING_BATCH_SIZE;

    if (remainder > 0) {
      batches++;
    }

    return (int) batches;
  }
}