/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package com.act.biointerpretation.Utils;
import act.shared.Organism;
import com.act.biointerpretation.test.util.MockedNoSQLAPI;
import org.junit.Before;
import org.junit.Test;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import static org.junit.Assert.assertEquals;
public class OrgMinimalPrefixGeneratorTest {
private MockedNoSQLAPI mockAPI;
private Map<String, String> minimalPrefixMapping;
@Before
public void setUp() {
Map<Long, String> testOrgNames = new HashMap<>();
testOrgNames.put(4000003474L, "Mus musculus");
testOrgNames.put(4000003475L, "Mus musculus sp.");
testOrgNames.put(4000003476L, "Mus musculus sp. 123");
testOrgNames.put(4000003477L, "Lactobacillus");
testOrgNames.put(4000003478L, "Lactobacillus buchneris");
testOrgNames.put(4000003479L, "Lactobacillus salivarius");
testOrgNames.put(4000003480L, "Lactobacillus sp. SK007");
testOrgNames.put(4000003481L, "Lactobacillus sp.");
testOrgNames.put(4000003482L, "Streptococcus");
testOrgNames.put(4000003483L, "Streptococcus mitior");
testOrgNames.put(4000003484L, "Streptococcus sanguinis");
testOrgNames.put(400008594L, "Homo sapiens");
mockAPI = new MockedNoSQLAPI();
mockAPI.installMocks(new ArrayList<>(), new ArrayList<>(), testOrgNames, new HashMap<>());
Iterator<Organism> orgIterator = mockAPI.getMockNoSQLAPI().readOrgsFromInKnowledgeGraph();
OrgMinimalPrefixGenerator prefixGenerator = new OrgMinimalPrefixGenerator(orgIterator);
minimalPrefixMapping = prefixGenerator.getMinimalPrefixMapping();
}
@Test
public void testMinimalPrefixMapping() {
assertEquals("testing minimal prefix mapping", "Mus musculus", minimalPrefixMapping.get("Mus musculus"));
assertEquals("testing minimal prefix mapping", "Mus musculus", minimalPrefixMapping.get("Mus musculus sp."));
assertEquals("testing minimal prefix mapping", "Mus musculus", minimalPrefixMapping.get("Mus musculus sp. 123"));
assertEquals("testing minimal prefix mapping", "Lactobacillus", minimalPrefixMapping.get("Lactobacillus"));
assertEquals("testing minimal prefix mapping", "Lactobacillus", minimalPrefixMapping.get("Lactobacillus buchneris"));
assertEquals("testing minimal prefix mapping", "Lactobacillus", minimalPrefixMapping.get("Lactobacillus salivarius"));
assertEquals("testing minimal prefix mapping", "Lactobacillus", minimalPrefixMapping.get("Lactobacillus sp. SK007"));
assertEquals("testing minimal prefix mapping", "Lactobacillus", minimalPrefixMapping.get("Lactobacillus sp."));
assertEquals("testing minimal prefix mapping", "Streptococcus", minimalPrefixMapping.get("Streptococcus"));
assertEquals("testing minimal prefix mapping", "Streptococcus", minimalPrefixMapping.get("Streptococcus mitior"));
assertEquals("testing minimal prefix mapping", "Streptococcus", minimalPrefixMapping.get("Streptococcus sanguinis"));
assertEquals("testing minimal prefix mapping", "Homo sapiens", minimalPrefixMapping.get("Homo sapiens"));
}
}