/*************************************************************************
* *
* 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 act.installer.pubchem;
import act.shared.Chemical;
import org.junit.Before;
import org.junit.Test;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import java.io.File;
import java.io.FileInputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.GZIPInputStream;
import static org.junit.Assert.assertEquals;
public class PubchemParserTest {
PubchemParser pubchemParser;
@Before
public void setUp() throws Exception {
pubchemParser = new PubchemParser(null);
pubchemParser.init();
}
@Test
public void testParserProcessesTheCorrectChemicals() throws Exception {
File testFile = new File(this.getClass().getResource("CompoundTest.xml.gz").getFile());
String expectedInchi1 = "InChI=1S/C18H27FN2/c1-2-14-11-17(20-16-5-3-4-6-16)13-21(12-14)18-9-7-15(19)8-10-18/h7-10,14,16-17,20H,2-6,11-13H2,1H3";
String expectedSmiles1 = "CCC1CC(CN(C1)C2=CC=C(C=C2)F)NC3CCCC3";
String expectedCanonicalName1 = "N-cyclopentyl-5-ethyl-1-(4-fluorophenyl)piperidin-3-amine";
Long expectedPubchemId1 = 84000001L;
Chemical testChemical1 = new Chemical(1L, expectedPubchemId1, expectedCanonicalName1, expectedSmiles1);
testChemical1.setInchi(expectedInchi1);
String expectedInchi2 = "InChI=1S/C16H23FN2/c17-13-5-3-9-16(11-13)19-10-4-8-15(12-19)18-14-6-1-2-7-14/h3,5,9,11,14-15,18H,1-2,4,6-8,10,12H2";
String expectedSmiles2 = "C1CCC(C1)NC2CCCN(C2)C3=CC(=CC=C3)F";
String expectedCanonicalName2 = "N-cyclopentyl-1-(3-fluorophenyl)piperidin-3-amine";
Long expectedPubchemId2 = 84000002L;
Chemical testChemical2 = new Chemical(2L, expectedPubchemId2, expectedCanonicalName2, expectedSmiles2);
testChemical2.setInchi(expectedInchi2);
List<Chemical> expectedChemicals = new ArrayList<>();
expectedChemicals.add(testChemical1);
expectedChemicals.add(testChemical2);
XMLInputFactory factory = XMLInputFactory.newInstance();
XMLEventReader eventReader = factory.createXMLEventReader(new GZIPInputStream(new FileInputStream(testFile)));
int counter = 0;
Chemical actualChemical;
while ((actualChemical = pubchemParser.extractNextChemicalFromXMLStream(eventReader)) != null) {
Chemical expectedChemical = expectedChemicals.get(counter);
assertEquals("Inchis parsed from the xml file should be the same as expected", expectedChemical.getInChI(), actualChemical.getInChI());
assertEquals("Canonical name parsed from the xml file should be the same as expected", expectedChemical.getCanon(), actualChemical.getCanon());
assertEquals("Smiles parsed from the xml file should be the same as expected", expectedChemical.getSmiles(), actualChemical.getSmiles());
assertEquals("Pubchem id parsed from the xml file should be the same as expected", expectedChemical.getPubchemID(), actualChemical.getPubchemID());
counter++;
}
assertEquals("Two chemicals should be parsed from the xml file", 2, counter);
}
}