/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.dev.db;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.feature.tribble.IGVBEDCodec;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import htsjdk.tribble.example.ExampleBinaryCodec;
import htsjdk.tribble.readers.PositionalBufferedStream;
import org.junit.Test;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.sql.ResultSet;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;
/**
* User: jacob
* Date: 2012-Aug-22
*/
public class SQLInputStreamTest extends AbstractHeadlessTest {
@Test
public void basicTestReadBinary() throws Exception {
ResultSet rs = DBManagerTest.getAllFromSQLTable("sql/unigene.db", "unigene");
SQLInputStream is = new SQLInputStream(rs, false, 1, 3);
FeatureCodec featCodec = new ExampleBinaryCodec();
PositionalBufferedStream pbs = new PositionalBufferedStream(is);
int count = 0;
while (!rs.isAfterLast()) {
Feature feat = featCodec.decode(pbs);
checkFeatureIntegrity(feat, "chr2");
count++;
}
assertEquals(72, count);
DBManager.closeAll(rs);
}
@Test
public void basicTestReadString() throws Exception {
ResultSet rs = DBManagerTest.getAllFromSQLTable("sql/unigene.db", "unigene");
InputStream is = new SQLInputStream(rs, true);
BufferedReader in = new BufferedReader(new InputStreamReader(is));
int totalLines = 0;
String val = "";
AsciiFeatureCodec featureCodec = new IGVBEDCodec(genome);
while ((val = in.readLine()) != null) {
Feature feat = featureCodec.decode(val);
checkFeatureIntegrity(feat, "chr2");
totalLines += 1;
}
assertEquals(72, totalLines);
DBManager.closeAll(rs);
}
private void checkFeatureIntegrity(Feature feat, String expChr) throws Exception {
assertEquals(expChr, feat.getChr());
assertTrue(feat.getEnd() > feat.getStart());
assertTrue(feat.getEnd() > 0);
assertTrue(feat.getStart() > 0);
}
}