package jalview.ext.ensembl;

import static org.testng.Assert.assertEquals;

import jalview.bin.Cache;
import jalview.ext.ensembl.EnsemblSpecies.EnsemblTaxon;

import java.util.List;
import java.util.Map;

import org.apache.log4j.Logger;
import org.testng.annotations.Test;

import junit.extensions.PA;

public class EnsemblSpeciesTest
{
  @Test(groups = "Network")
  public void testGetSpecies_ensembl()
  {
    Cache.log = Logger.getRootLogger();
    EnsemblSpecies species = EnsemblSpecies.getSpecies(true);
    System.out.println("Ensembllookup map size = "
            + ((Map) PA.getValue(species, "lookup")).size());

    List<EnsemblTaxon> matches = species.getNameMatches("homo sapiens");
    assertEquals(matches.size(), 1);
    EnsemblTaxon match = matches.get(0);
    assertEquals(match.ncbiId, "9606");

    matches = species.getNameMatches("mus ");
    assertEquals(matches.size(), 6);
    match = matches.get(0);
    assertEquals(match.ncbiId, "10089");
    assertEquals(match.name, "mus_caroli");
    match = matches.get(1);
    assertEquals(match.ncbiId, "10090");
    assertEquals(match.commonName, "house mouse");
    match = matches.get(2);
    assertEquals(match.ncbiId, "10091");
    assertEquals(match.displayName, "Mouse CAST/EiJ");
    assertEquals(match.commonName, "south eastern house mouse");
  }

  @Test(groups = "Network")
  public void testGetSpecies_ensemblGenomes()
  {
    Cache.log = Logger.getRootLogger();
    EnsemblSpecies species = EnsemblSpecies.getSpecies(false);
    System.out.println("EnsemblGenomes lookup map size = "
            + ((Map) PA.getValue(species, "lookup")).size());

    List<EnsemblTaxon> matches = species.getNameMatches("streptomyces al");
    assertEquals(matches.size(), 12);
    assertEquals(matches.get(0).ncbiId, "132473");
    assertEquals(matches.get(0).name, "streptomyces_alboniger");
    assertEquals(matches.get(1).ncbiId, "68570");
    assertEquals(matches.get(1).displayName, "Streptomyces albulus");
    assertEquals(matches.get(2).ncbiId, "68570");
    assertEquals(matches.get(2).name, "streptomyces_albulus_gca_001646665");
  }
}