/*
* Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
* Copyright [2016-2017] EMBL-European Bioinformatics Institute
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ensembl.healthcheck.test;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import org.ensembl.healthcheck.Species;
import org.testng.Assert;
import org.testng.annotations.Test;
public class SpeciesTest {
// -----------------------------------------------------------------
@Test
public void testToString() {
assertEquals("homo_sapiens", Species.HOMO_SAPIENS.toString(), "toString method not returning expected result");
}
// -----------------------------------------------------------------
@Test
public void testEquals() {
Assert.assertEquals(Species.HOMO_SAPIENS, Species.HOMO_SAPIENS, "equals method not working");
Assert.assertTrue(Species.TAKIFUGU_RUBRIPES != Species.CAENORHABDITIS_BRIGGSAE, "species that are the not the same are coming out equal");
}
// -----------------------------------------------------------------
@Test
public void testAlias() {
// not an exhaustive list ...
assertEquals(Species.resolveAlias("human"), Species.HOMO_SAPIENS);
assertEquals(Species.resolveAlias("rat"), Species.RATTUS_NORVEGICUS);
assertEquals(Species.resolveAlias("mus_musculus"), Species.MUS_MUSCULUS);
assertEquals(Species.resolveAlias("tetraodon_nigroviridis"), Species.TETRAODON_NIGROVIRIDIS);
assertEquals(Species.resolveAlias("apis_mellifera"), Species.APIS_MELLIFERA);
assertEquals(Species.resolveAlias("ciona_intestinalis"), Species.CIONA_INTESTINALIS);
assertEquals(Species.resolveAlias("littlegreenman"), Species.UNKNOWN);
}
// -----------------------------------------------------------------
@Test
public void testTaxonomyIDs() {
assertEquals(Species.getTaxonomyID(Species.HOMO_SAPIENS), "9606");
assertEquals(Species.getTaxonomyID(Species.DANIO_RERIO), "7955");
assertEquals(Species.getTaxonomyID(Species.TETRAODON_NIGROVIRIDIS), "99883");
assertEquals(Species.getTaxonomyID(Species.CIONA_INTESTINALIS), "7719");
assertEquals(Species.getTaxonomyID(Species.APIS_MELLIFERA), "7460");
assertEquals("0", Species.getTaxonomyID(Species.UNKNOWN), "Checking unknown returns a taxon of 0");
}
// -----------------------------------------------------------------
@Test
public void testSimilarNames() {
assertTrue(!(Species.resolveAlias("hedgehog").equals(Species.ECHINOPS_TELFAIRI)));
assertTrue(Species.resolveAlias("hedgehog").equals(Species.ERINACEUS_EUROPAEUS));
}
// -----------------------------------------------------------------
@Test
public void testAssemblyPrefixes() {
assertEquals(Species.getSpeciesForAssemblyPrefix("GRCh"), Species.HOMO_SAPIENS);
}
// -----------------------------------------------------------------
}