@Override public Query query() { return new QueryImpl(this); }
private boolean isGenomeBrowserEntity(EntityMetaData entityMetaData) { AttributeMetaData attributeStartPosition = genomeConfig.getAttributeMetadataForAttributeNameArray( GenomeConfig.GENOMEBROWSER_POS, entityMetaData); AttributeMetaData attributeChromosome = genomeConfig.getAttributeMetadataForAttributeNameArray( GenomeConfig.GENOMEBROWSER_CHROM, entityMetaData); return attributeStartPosition != null && attributeChromosome != null; }
boolean isXrefOrCategorialDataType(Attribute attribute) { return isSingleReferenceType(attribute); }
public AggregateQueryRsqlVisitor(EntityType entityType, Query<Entity> query) { this.entityType = checkNotNull(entityType); this.aggsQ = new AggregateQueryImpl().query(query); }
/** * create a new entity based on the merged entity metadata */ private AbstractEntity createMergedEntity(List<AttributeMetaData> commonAttributes, Entity entity) { AbstractEntity mergedEntity = new MapEntity(ID); mergedEntity.set(ID, UUID.randomUUID().toString()); for (AttributeMetaData attributeMetaData : commonAttributes) { mergedEntity.set(attributeMetaData.getName(), entity.get(attributeMetaData.getName())); } return mergedEntity; }
@Override public <E extends Entity> Iterable<E> findAll(Query q, Class<E> clazz) { return new ConvertingIterable<E>(clazz, findAll(q)); }
EntityType toEntityTypeReference(String entityTypeId) { if (entityTypeId == null) { return null; } return new EntityType(new LazyEntity(entityTypeMetadata, dataService, entityTypeId)); }
@Override public Query<Entity> createQuery(Entity entity) { Object value = entity.get(EffectsMetaData.GENE_NAME); return EQ(EffectsMetaData.GENE_NAME, value); } }
public boolean hasSelfReferences() { return EntityTypeUtils.hasSelfReferences(getTarget()); } }
public String getAttributeName(String attribute, String fieldName, Entity entity) { if (attribute == null) { attribute = config.getAttributeNameForAttributeNameArray(fieldName, entity.getEntityType()); } return attribute; }
@Override public Query query() { return new QueryImpl(this); }
@Override public <E extends Entity> Iterable<E> findAll(Iterable<Object> ids, Class<E> clazz) { return new ConvertingIterable<E>(clazz, findAll(ids)); }
@Override public long count() { return count(new QueryImpl()); }
@Override public Long load(String ontologyIri) { Entity ontologyEntity = dataService.findOne( ONTOLOGY, new QueryImpl<>().eq(OntologyMetaData.ONTOLOGY_IRI, ontologyIri)); if (ontologyEntity != null) { return dataService.count( ONTOLOGY_TERM, new QueryImpl<>().eq(OntologyTermMetaData.ONTOLOGY, ontologyEntity)); } return (long) 0; } });
@Override public <E extends Entity> Iterable<E> iterator(Class<E> clazz) { return findAll(new QueryImpl(), clazz); }
/** * Helper class to count the number of observationSets in a dataset, in * another word the number of rows in a dataset * * @param sourceDataSetId * @return */ private long countRowsByDataSet(Integer sourceDataSetId) { DataSet sourceDataSet = dataService.findOne(DataSet.ENTITY_NAME, sourceDataSetId, DataSet.class); return dataService.count(ObservationSet.ENTITY_NAME, new QueryImpl().eq(ObservationSet.PARTOFDATASET, sourceDataSet)); } }