GeneIdentifierDaoImpl.java

package org.nextprot.api.core.dao.impl;

import org.nextprot.api.commons.spring.jdbc.DataSourceServiceLocator;
import org.nextprot.api.commons.utils.SQLDictionary;
import org.nextprot.api.core.dao.GeneIdentifierDao;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.stereotype.Repository;

import java.util.*;

@Repository
public class GeneIdentifierDaoImpl implements GeneIdentifierDao {

	@Autowired private SQLDictionary sqlDictionary;

	@Autowired private DataSourceServiceLocator dsLocator;

	@Override
	public Set<String> findGeneNames() {
		return new TreeSet<>(new JdbcTemplate(dsLocator.getDataSource()).queryForList(sqlDictionary.getSQLQuery("all-gene-names"), String.class));
	}

	@Override
	public Map<String, List<String>> findEntryGeneNames() {

		Map<String, List<String>> map = new TreeMap<>();

		new JdbcTemplate(dsLocator.getDataSource()).queryForList(sqlDictionary.getSQLQuery("all-accessions-with-gene-names"))
				.forEach(row -> {
					String entryName = (String) row.get("unique_name");

					if (!map.containsKey(entryName)) {
						map.put(entryName, new ArrayList<>());
					}
					map.get(entryName).add((String) row.get("gene_name"));
				});

		map.values().forEach(geneNames -> geneNames.sort(String::compareTo));

		return map;
	}
}