private ScheduledJob getJob(String scheduledJobId) { ScheduledJob scheduledJob = dataService.findOneById(SCHEDULED_JOB, scheduledJobId, ScheduledJob.class); if (scheduledJob == null) { throw new UnknownEntityException(SCHEDULED_JOB, scheduledJobId); } return scheduledJob; }
/** * @param folderId <tt>null</tt> implies the root folder * @return package or <tt>null</tt> for the root package */ private @Nullable Package getPackage(@Nullable String folderId) { if (folderId == null) { return null; } Package aPackage = dataService.findOneById(PackageMetadata.PACKAGE, folderId, Package.class); if (aPackage == null) { throw new UnknownEntityException(PackageMetadata.PACKAGE, folderId); } return aPackage; } }
@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); }
@Override @PreAuthorize("hasAnyRole('ROLE_SYSTEM, ROLE_SU, ROLE_PLUGIN_WRITE_menumanager')") @Transactional public MappingProject cloneMappingProject(String mappingProjectId, String clonedMappingProjectName) { MappingProject mappingProject = mappingProjectRepository.getMappingProject(mappingProjectId); if (mappingProject == null) { throw new UnknownEntityException("Mapping project [" + mappingProjectId + "] does not exist"); } return cloneMappingProject(mappingProject, clonedMappingProjectName); }
@Override public void addAttribute(String entityName, AttributeMetaData attribute) { DefaultEntityMetaData entityMetaData; try { entityMetaData = (DefaultEntityMetaData) dataService.getEntityMetaData(entityName); } catch (ClassCastException ex) { throw new RuntimeException("Cannot cast EntityMetaData to DefaultEntityMetadata " + ex); } if (entityMetaData == null) throw new UnknownEntityException(String.format("Unknown entity '%s'", entityName)); entityMetaData.addAttributeMetaData(attribute); }
@Override public RepositoryAnnotator getAnnotatorByName(String annotatorName) { getAllAnnotators(); for (RepositoryAnnotator annotator : annotators) { if (annotator.getSimpleName().equalsIgnoreCase(annotatorName)) { return annotator; } } throw new UnknownEntityException("Unknown annotator [" + annotatorName + "]"); }
@GetMapping(produces = TEXT_TURTLE_VALUE, value = "/{catalogID}/{datasetID}") @ResponseBody @RunAsSystem public Model getDataset( @PathVariable("catalogID") String catalogID, @PathVariable("datasetID") String datasetID) { String subjectIRI = getBaseUri().pathSegment(catalogID, datasetID).toUriString(); Entity subjectEntity = dataService.findOneById("fdp_Dataset", datasetID); if (subjectEntity == null) { throw new UnknownEntityException("fdp_Dataset", datasetID); } return entityModelWriter.createRdfModel(subjectIRI, subjectEntity); }
@Override public Iterable<SemanticTag<Package, OntologyTerm, Ontology>> getTagsForPackage( Package aPackage) { Entity packageEntity = dataService.findOneById(PACKAGE, aPackage.getId()); if (packageEntity == null) { throw new UnknownEntityException(PACKAGE, aPackage.getId()); } List<SemanticTag<Package, OntologyTerm, Ontology>> tags = Lists.newArrayList(); for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) { tags.add(asTag(aPackage, tagEntity)); } return tags; }
private OidcClient getOidcClient(OidcUserRequest userRequest) { String registrationId = userRequest.getClientRegistration().getRegistrationId(); OidcClient oidcClient = dataService.findOneById(OidcClientMetadata.OIDC_CLIENT, registrationId, OidcClient.class); if (oidcClient == null) { throw new UnknownEntityException(OidcClientMetadata.OIDC_CLIENT, registrationId); } return oidcClient; } }
@GetMapping(produces = TEXT_TURTLE_VALUE, value = "/{catalogID}") @ResponseBody @RunAsSystem public Model getCatalog(@PathVariable("catalogID") String catalogID) { String subjectIRI = getBaseUri().pathSegment(catalogID).toUriString(); Entity subjectEntity = dataService.findOneById("fdp_Catalog", catalogID); if (subjectEntity == null) { throw new UnknownEntityException("fdp_Catalog", catalogID); } return entityModelWriter.createRdfModel(subjectIRI, subjectEntity); }
@Override public Iterable<SemanticTag<Package, OntologyTerm, Ontology>> getTagsForPackage(Package package_) { Entity packageEntity = dataService.findOneById(PACKAGE, package_.getId()); if (packageEntity == null) { throw new UnknownEntityException("Unknown package [" + package_.getId() + "]"); } List<SemanticTag<Package, OntologyTerm, Ontology>> tags = Lists.newArrayList(); for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) { tags.add(asTag(package_, tagEntity)); } return tags; }
@Override public void deleteById(Object id) { Package aPackage = findOneById(id); if (aPackage == null) { throw new UnknownEntityException(getEntityType(), id); } packageValidator.validate(aPackage); super.deleteById(id); }
@Override public void deleteAttribute(String entityName, String attributeName) { EntityMetaData entityMetaData = dataService.getMeta().getEntityMetaData(entityName); if (entityMetaData == null) throw new UnknownEntityException(String.format("Unknown entity '%s'", entityName)); DefaultEntityMetaData defaultEntityMetaData = new DefaultEntityMetaData( dataService.getMeta().getEntityMetaData(entityName)); AttributeMetaData attr = entityMetaData.getAttribute(attributeName); if (attr == null) throw new UnknownAttributeException( String.format("Unknown attribute '%s' of entity '%s'", attributeName, entityName)); defaultEntityMetaData.removeAttributeMetaData(attr); }
@Override @RunAsSystem public Iterable<SemanticTag<Package, LabeledResource, LabeledResource>> getTagsForPackage( Package p) { Entity packageEntity = dataService.findOne(PACKAGE, new QueryImpl<>().eq(PackageMetadata.ID, p.getId())); if (packageEntity == null) { throw new UnknownEntityException(PACKAGE, p.getId()); } List<SemanticTag<Package, LabeledResource, LabeledResource>> tags = Lists.newArrayList(); for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) { tags.add(SemanticTag.asTag(p, tagEntity)); } return tags; }
@Override @RunAsSystem public Iterable<SemanticTag<Package, LabeledResource, LabeledResource>> getTagsForPackage(Package p) { Entity packageEntity = dataService .findOne(PACKAGE, new QueryImpl<>().eq(PackageMetadata.ID, p.getId())); if (packageEntity == null) { throw new UnknownEntityException("Unknown package [" + p.getId() + "]"); } List<SemanticTag<Package, LabeledResource, LabeledResource>> tags = Lists.newArrayList(); for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) { tags.add(SemanticTag.asTag(p, tagEntity)); } return tags; }
private void updatePackage(Resource resource) { Package aPackage = dataService.findOneById(PackageMetadata.PACKAGE, resource.getId(), Package.class); if (aPackage == null) { throw new UnknownEntityException(PackageMetadata.PACKAGE, resource.getId()); } if (!Objects.equal(aPackage.getLabel(), resource.getLabel()) || !Objects.equal(aPackage.getDescription(), resource.getDescription())) { aPackage.setLabel(resource.getLabel()); aPackage.setDescription(resource.getDescription()); dataService.update(PackageMetadata.PACKAGE, aPackage); } }
private void updateEntityType(Resource resource) { EntityType entityType = dataService.findOneById(ENTITY_TYPE_META_DATA, resource.getId(), EntityType.class); if (entityType == null) { throw new UnknownEntityException(ENTITY_TYPE_META_DATA, resource.getId()); } if (!Objects.equal(entityType.getLabel(), resource.getLabel()) || !Objects.equal(entityType.getDescription(), resource.getDescription())) { entityType.setLabel(resource.getLabel()); entityType.setDescription(resource.getDescription()); dataService.update(ENTITY_TYPE_META_DATA, entityType); } }
/** * Executes a {@link ScheduledJob} in the current thread. * * @param scheduledJobId ID of the {@link ScheduledJob} to run */ @RunAsSystem public void executeScheduledJob(String scheduledJobId) { ScheduledJob scheduledJob = dataService.findOneById(SCHEDULED_JOB, scheduledJobId, ScheduledJob.class); if (scheduledJob == null) { throw new UnknownEntityException(SCHEDULED_JOB, scheduledJobId); } JobExecution jobExecution = createJobExecution(scheduledJob); Job molgenisJob = saveExecutionAndCreateJob(jobExecution); try { runJob(jobExecution, molgenisJob); } catch (Exception ex) { LOG.error("Error creating job for JobExecution.", ex); jobExecution.setStatus(JobExecution.Status.FAILED); jobExecution.setProgressMessage(ex.getMessage()); dataService.update(jobExecution.getEntityType().getId(), jobExecution); throw ex; } }
private Map<String, Object> getEntityResponse( String entityTypeId, String untypedId, AttributeFilter attributeFilter, boolean includeCategories) { EntityType entityType = dataService.getEntityType(entityTypeId); Object id = getTypedValue(untypedId, entityType.getIdAttribute()); Fetch fetch = AttributeFilterToFetchConverter.convert( attributeFilter, entityType, LanguageService.getCurrentUserLanguageCode()); Entity entity = dataService.findOneById(entityTypeId, id, fetch); if (entity == null) { throw new UnknownEntityException(entityType, id); } return createEntityResponse(entity, fetch, true, includeCategories); }
private void updateInternal( String entityTypeId, String untypedId, Map<String, Object> entityMap) { EntityType meta = dataService.getEntityType(entityTypeId); if (meta.getIdAttribute() == null) { throw new IllegalArgumentException(entityTypeId + " does not have an id attribute"); } Object id = getTypedValue(untypedId, meta.getIdAttribute()); Entity existing = dataService.findOneById( entityTypeId, id, new Fetch().field(meta.getIdAttribute().getName())); if (existing == null) { throw new UnknownEntityException(meta, id); } Entity entity = this.restService.toEntity(meta, entityMap); dataService.update(entityTypeId, entity); restService.updateMappedByEntities(entity, existing); }