OntologyServiceImpl.java

package org.molgenis.ontology.core.service.impl;

import org.elasticsearch.common.collect.Lists;
import org.molgenis.ontology.core.model.Ontology;
import org.molgenis.ontology.core.model.OntologyTerm;
import org.molgenis.ontology.core.repository.OntologyRepository;
import org.molgenis.ontology.core.repository.OntologyTermRepository;
import org.molgenis.ontology.core.service.OntologyService;
import org.springframework.beans.factory.annotation.Autowired;

import java.util.ArrayList;
import java.util.List;
import java.util.Set;

import static java.util.Objects.requireNonNull;
import static java.util.stream.Collectors.toList;

public class OntologyServiceImpl implements OntologyService
{
	private OntologyRepository ontologyRepository;
	private OntologyTermRepository ontologyTermRepository;

	@Autowired
	public OntologyServiceImpl(OntologyRepository ontologyRepository, OntologyTermRepository ontologyTermRepository)
	{
		this.ontologyRepository = requireNonNull(ontologyRepository);
		this.ontologyTermRepository = requireNonNull(ontologyTermRepository);
	}

	@Override
	public List<Ontology> getOntologies()
	{
		return ontologyRepository.getOntologies().collect(toList());
	}

	@Override
	public List<String> getAllOntologiesIds()
	{
		final List<String> allOntologiesIds = new ArrayList<String>();
		ontologyRepository.getOntologies().forEach(e -> allOntologiesIds.add(e.getId()));
		return allOntologiesIds;
	}

	@Override
	public Ontology getOntology(String name)
	{
		return ontologyRepository.getOntology(name);
	}

	@Override
	public OntologyTerm getOntologyTerm(String iri)
	{
		return ontologyTermRepository.getOntologyTerm(iri.split(","));

	}

	@Override
	public List<OntologyTerm> getAllOntologyTerms(String ontologyIri)
	{
		return ontologyTermRepository.getAllOntologyTerms(ontologyIri);
	}

	@Override
	public List<OntologyTerm> findExcatOntologyTerms(List<String> ontologyIds, Set<String> terms, int pageSize)
	{
		if (null == terms || terms.size() == 0)
		{
			return Lists.<OntologyTerm>newArrayList();
		}
		return ontologyTermRepository.findExcatOntologyTerms(ontologyIds, terms, pageSize);
	}

	@Override
	public List<OntologyTerm> findOntologyTerms(List<String> ontologyIds, Set<String> terms, int pageSize)
	{
		if (null == terms || terms.size() == 0)
		{
			return Lists.<OntologyTerm>newArrayList();
		}
		return ontologyTermRepository.findOntologyTerms(ontologyIds, terms, pageSize);
	}

	@Override
	public List<OntologyTerm> getChildren(OntologyTerm ontologyTerm)
	{
		return ontologyTermRepository.getChildren(ontologyTerm);
	}

	@Override
	public Integer getOntologyTermDistance(OntologyTerm ontologyTerm1, OntologyTerm ontologyTerm2)
	{
		return ontologyTermRepository.getOntologyTermDistance(ontologyTerm1, ontologyTerm2);
	}
}