@Override public boolean sourceExists() { return resources.hasRepository(sourceRepositoryName) || dataService.hasRepository(sourceRepositoryName); }
@Override public boolean hasRepository(String entityTypeId) { getResources(); return dataService.hasRepository(entityTypeId) || (resources.containsKey(entityTypeId) && resources.get( entityTypeId).isAvailable()); }
@Override public String canAnnotate(EntityType repoMetaData) { if (dataService.hasRepository(repoMetaData.getId() + SnpEffRunner.ENTITY_NAME_SUFFIX)) { return "already annotated with SnpEff"; } else { return super.canAnnotate(repoMetaData); } }
private Entity getPluginSettings(String entityTypeId) { return dataService.hasRepository(entityTypeId) ? dataService.findOneById(entityTypeId, getId()) : null; }
private void tryDeleteRepository(String entityTypeId) { if (dataService.hasRepository(entityTypeId) && permissionService.hasPermission( new EntityTypeIdentity(entityTypeId), EntityTypePermission.DELETE_METADATA)) { RunAsSystemAspect.runAsSystem(() -> deleteRepository(entityTypeId)); } else { LOG.info("Unable to delete repository {}", entityTypeId); } }
Writer w = env.getOut(); if (dataService.hasRepository(dataset) && (dataexplorer != null))
if (selectedEntityName != null) entityExists = dataService.hasRepository(selectedEntityName); hasEntityPermission = molgenisPermissionService.hasPermissionOnEntity(selectedEntityName, Permission.COUNT);
private Repository<Entity> getTargetRepository(String entityTypeId, EntityType targetMetadata) { Repository<Entity> targetRepo; if (!dataService.hasRepository(entityTypeId)) { targetRepo = addTargetEntityType(targetMetadata); } else { targetRepo = dataService.getRepository(entityTypeId); compareTargetMetadatas(targetRepo.getEntityType(), targetMetadata); } return targetRepo; }
private Repository<Entity> getTargetRepository(String entityTypeId, EntityType targetMetadata) { Repository<Entity> targetRepo; if (!dataService.hasRepository(entityTypeId)) { targetRepo = addTargetEntityType(targetMetadata); } else { targetRepo = dataService.getRepository(entityTypeId); compareTargetMetadatas(targetRepo.getEntityType(), targetMetadata); } return targetRepo; }
if (!dataService.hasRepository(ontologyName))
/** * Cleans up successful IndexJobExecutions that finished longer than five minutes ago. delay for a * minute to allow the transaction manager to become available */ @Scheduled(initialDelay = 1 * 60 * 1000, fixedRate = 5 * 60 * 1000) public void cleanupJobExecutions() { runAsSystem( () -> { LOG.trace("Clean up Index job executions..."); Instant fiveMinutesAgo = Instant.now().minus(5, ChronoUnit.MINUTES); boolean indexJobExecutionExists = dataService.hasRepository(IndexJobExecutionMeta.INDEX_JOB_EXECUTION); if (indexJobExecutionExists) { Stream<Entity> executions = dataService .getRepository(IndexJobExecutionMeta.INDEX_JOB_EXECUTION) .query() .lt(END_DATE, fiveMinutesAgo) .and() .eq(STATUS, SUCCESS.toString()) .findAll(); dataService.delete(IndexJobExecutionMeta.INDEX_JOB_EXECUTION, executions); LOG.debug("Cleaned up Index job executions."); } else { LOG.warn("{} does not exist", IndexJobExecutionMeta.INDEX_JOB_EXECUTION); } }); } }
/** * Creates a fully reconstructed MappingProject from an Entity retrieved from the repository. * * @param mappingTargetEntity Entity with {@link MappingProjectMetaData} metadata * @return fully reconstructed MappingProject */ private MappingTarget toMappingTarget(Entity mappingTargetEntity) { List<EntityMapping> entityMappings = Collections.emptyList(); String identifier = mappingTargetEntity.getString(MappingTargetMetaData.IDENTIFIER); if (!dataService.hasRepository(mappingTargetEntity.getString(MappingTargetMetaData.TARGET))) { return null; } EntityType target = dataService.getEntityType(mappingTargetEntity.getString(MappingTargetMetaData.TARGET)); if (mappingTargetEntity.getEntities(MappingTargetMetaData.ENTITY_MAPPINGS) != null) { List<Entity> entityMappingEntities = Lists.newArrayList( mappingTargetEntity.getEntities(MappingTargetMetaData.ENTITY_MAPPINGS)); entityMappings = entityMappingRepository.toEntityMappings(entityMappingEntities); } return new MappingTarget(identifier, target, entityMappings); } }
/** * Creates a fully reconstructed MappingProject from an Entity retrieved from the repository. * * @param mappingTargetEntity Entity with {@link MappingProjectMetaData} metadata * @return fully reconstructed MappingProject */ private MappingTarget toMappingTarget(Entity mappingTargetEntity) { List<EntityMapping> entityMappings = Collections.emptyList(); String identifier = mappingTargetEntity.getString(MappingTargetMetaData.IDENTIFIER); if (!dataService.hasRepository(mappingTargetEntity.getString(MappingTargetMetaData.TARGET))) { return null; } EntityType target = dataService .getEntityType(mappingTargetEntity.getString(MappingTargetMetaData.TARGET)); if (mappingTargetEntity.getEntities(MappingTargetMetaData.ENTITY_MAPPINGS) != null) { List<Entity> entityMappingEntities = Lists .newArrayList(mappingTargetEntity.getEntities(MappingTargetMetaData.ENTITY_MAPPINGS)); entityMappings = entityMappingRepository.toEntityMappings(entityMappingEntities); } return new MappingTarget(identifier, target, entityMappings); } }
if (dataService.hasRepository(userGivenName)) { result.addError(new ObjectError("wizard", "An entity with this name already exists.")); return null;
if (!dataService.hasRepository(entityTypeId) || dataService.count(entityTypeId, new QueryImpl<>()) == 0) return false;
throws Exception { if (!dataService.hasRepository(entityTypeId)) throw new UnknownEntityTypeException(entityTypeId); EntityTypeUtils.buildFullName( repositoryToCopyFrom.getEntityType().getPackage(), request.getNewEntityName()); if (dataService.hasRepository(newFullName)) { throw new RepositoryAlreadyExistsException(newFullName);
if (dataService.hasRepository(entityTypeId)) { EntityType entityType = dataService
if (!dataService.hasRepository(targetMetaData.getId()))
if (dataService.hasRepository(ontologyEntityName))
private DataSet createDerivedDataSets(String userName, Integer targetDataSetId, List<Integer> sourceDataSetIds) { DataSet targetDataSet = dataService.findOne(DataSet.ENTITY_NAME, targetDataSetId, DataSet.class); DataSet derivedDataSet = new DataSet(); derivedDataSet.setIdentifier(createDerivedDataSetIdentifier(userName, targetDataSet.getId().toString(), sourceDataSetIds)); derivedDataSet.setName(createDerivedDataSetName(userName, targetDataSet.getName())); derivedDataSet.setProtocolUsed(targetDataSet.getProtocolUsed()); dataService.add(DataSet.ENTITY_NAME, derivedDataSet); dataService.getCrudRepository(DataSet.ENTITY_NAME).flush(); if (!dataService.hasRepository(derivedDataSet.getIdentifier())) { dataService.addRepository(new OmxRepository(dataService, searchService, derivedDataSet.getIdentifier(), new DefaultEntityValidator(dataService, new EntityAttributesValidator()))); } return derivedDataSet; }