Examples with RunAsSystem org.molgenis.security.core.runas.RunAsSystem used on opensource projects

Example 26 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class OntologyTermFrequencyServiceImpl method updateTermFrequency.

@Override
@Async
@RunAsSystem
public void updateTermFrequency() {
    // Remove all the existing term frequency records
    dataService.deleteAll(TERM_FREQUENCY);
    List<Entity> entitiesToAdd = new ArrayList<>();
    // Create new term frequency records
    dataService.findAll(ONTOLOGY_TERM_SYNONYM).forEach(entity -> {
        String ontologyTermSynonym = entity.getString(OntologyTermSynonymMetaData.ONTOLOGY_TERM_SYNONYM_ATTR);
        PubMedTFEntity pubMedTFEntity = pubMedTermFrequencyService.getTermFrequency(ontologyTermSynonym);
        if (pubMedTFEntity != null) {
            // FIXME remove reference to getApplicationContext
            TermFrequencyMetaData termFrequencyEntityType = getApplicationContext().getBean(TermFrequencyMetaData.class);
            Entity mapEntity = new DynamicEntity(termFrequencyEntityType);
            mapEntity.set(TERM, ontologyTermSynonym);
            mapEntity.set(FREQUENCY, pubMedTFEntity.getFrequency());
            mapEntity.set(OCCURRENCE, pubMedTFEntity.getOccurrence());
            entitiesToAdd.add(mapEntity);
            if (entitiesToAdd.size() > BATCH_SIZE) {
                dataService.add(TERM_FREQUENCY, entitiesToAdd.stream());
                entitiesToAdd.clear();
            }
        }
    });
    if (!entitiesToAdd.isEmpty()) {
        dataService.add(TERM_FREQUENCY, entitiesToAdd.stream());
    }
}

Example 27 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class FairController method getDistribution.

@GetMapping(produces = TEXT_TURTLE_VALUE, value = "/{catalogID}/{datasetID}/{distributionID}")
@ResponseBody
@RunAsSystem
public Model getDistribution(@PathVariable("catalogID") String catalogID, @PathVariable("datasetID") String datasetID, @PathVariable("distributionID") String distributionID) {
    String subjectIRI = getBaseUri().pathSegment(catalogID, datasetID, distributionID).toUriString();
    Entity subjectEntity = dataService.findOneById("fdp_Distribution", distributionID);
    return entityModelWriter.createRdfModel(subjectIRI, subjectEntity);
}

Example 28 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class FairController method getCatalog.

@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(format("Catalog with id [%s] does not exist", catalogID));
    }
    return entityModelWriter.createRdfModel(subjectIRI, subjectEntity);
}

Example 29 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class UntypedTagService method getTagsForEntity.

@Override
@RunAsSystem
public Iterable<SemanticTag<EntityType, LabeledResource, LabeledResource>> getTagsForEntity(EntityType entityType) {
    List<SemanticTag<EntityType, LabeledResource, LabeledResource>> result = new ArrayList<>();
    Entity entity = findEntity(entityType);
    if (entity == null) {
        LOG.warn("No known entity with name " + entityType.getId() + ".");
    } else {
        for (Entity tagEntity : entity.getEntities(EntityTypeMetadata.TAGS)) {
            result.add(SemanticTag.asTag(entityType, tagEntity));
        }
    }
    return result;
}