/*
* 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.BasicFeature;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.tribble.UCSCGeneTableCodec;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.Feature;
import org.junit.Assume;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import static junit.framework.Assert.*;
/**
* Test our profiles contacting UCSC database
* User: jacob
* Date: 2012/05/29
*/
public class UCSC_SQL_Test extends AbstractHeadlessTest {
private static final String UCSC_HOST = "genome-mysql.cse.ucsc.edu";
private String profilePath = TestUtils.DATA_DIR + "sql/UCSC_profiles.dbxml";
private static void checkConnectUCSC() throws Exception {
boolean succeeded = false;
try {
String testPath = DBManager.createConnectionURL("mysql", UCSC_HOST, "hg18", null);
ResourceLocator locator = new ResourceLocator(testPath);
locator.setUsername("genome");
DBManager.getConnection(locator);
succeeded = true;
} catch (Exception e) {
e.printStackTrace();
}
Assume.assumeTrue(succeeded);
}
@BeforeClass
public static void setUpClass() throws Exception {
AbstractHeadlessTest.setUpClass();
checkConnectUCSC();
}
@Test
public void testLoadUCSC() throws Exception {
AsciiFeatureCodec codec = new UCSCGeneTableCodec(UCSCGeneTableCodec.Type.UCSCGENE, genome);
String host = UCSC_HOST;
String path = "hg18";
String port = null;
String url = DBManager.createConnectionURL("mysql", host, path, port);
ResourceLocator locator = new ResourceLocator(url);
locator.setUsername("genome");
String tableName = "knownGene";
int strt = 100000;
int end = 400000;
DBProfile.DBTable table = new DBProfile.DBTable(locator, tableName, "n/a", null, SQLCodecSource.UCSC_CHROMO_COL, SQLCodecSource.UCSC_START_COL, SQLCodecSource.UCSC_END_COL, 1, Integer.MAX_VALUE, null, null, null);
SQLCodecSource reader = new SQLCodecSource(table, codec);
Iterator<Feature> SQLFeatures = reader.getFeatures("chr1", strt, end);
int count = 0;
while (SQLFeatures.hasNext()) {
SQLFeatures.next();
count++;
}
assertEquals(12, count);
/**
* We should be getting unique names only
*/
List<String> names = reader.getSequenceNames();
assertTrue(names.size() > 0);
Set<String> set = new HashSet<String>(names);
assertEquals(names.size(), set.size());
}
@Test
public void testLoadUCSCFromProfileGene() throws Exception {
tstLoadFromProfile(profilePath, "knownGene");
}
@Test
public void testLoadUCSCFromProfileBED() throws Exception {
tstLoadFromProfile(profilePath, "affyExonTissues");
}
@Test
public void testLoadUCSCFromProfilePSL() throws Exception {
tstLoadFromProfile(profilePath, "all_mrna");
}
@Test
public void testLoadUCSCFromProfileSNP() throws Exception {
SQLCodecSource source = tstLoadFromProfile(profilePath, "snp126");
Iterator<Feature> feats = source.getFeatures("chr2", 10000, 100000);
int count = 0;
while (feats.hasNext()) {
BasicFeature f = (BasicFeature) feats.next();
assertEquals(0.0f, f.getScore());
assertFalse(f.hasExons());
assertNotSame(Strand.NONE, f.getStrand());
count++;
}
assertTrue(count > 0);
}
public SQLCodecSource tstLoadFromProfile(String profilePath, String tableName) throws Exception {
SQLCodecSource source = SQLCodecSource.getFromProfile(profilePath, tableName);
if (source == null) {
throw new RuntimeException("Table " + tableName + " not found in profile " + profilePath);
}
int start = 1;
int end = 100000;
Iterator<Feature> feats = source.getFeatures("chr1", start, end);
int count = 0;
while (feats.hasNext()) {
Feature f = feats.next();
assertTrue(f.getStart() >= start);
assertTrue(f.getStart() < end);
count++;
}
assertTrue("No data retrieved", count > 0);
return source;
}
@Test
public void testQueryWithBins() throws Exception {
tstQueryWithBins(profilePath, "all_mrna", "chr3", 500, 500000);
}
@Ignore("Fails sometimes and we're not sure why, but functionality isn't supported yet")
@Test
public void testQueryWithBins_big() throws Exception {
tstQueryWithBins(profilePath, "all_mrna", "chr1", 0, (int) 247e4);
}
public void tstQueryWithBins(String profilePath, String tableName, String chr, int start, int end) throws Exception {
int featWindowSize = (end - start) * 2;
SQLCodecSource binSource = SQLCodecSource.getFromProfile(profilePath, tableName);
binSource.setFeatureWindowSize(featWindowSize);
assertNotNull(binSource.binColName);
SQLCodecSource noBinSource = SQLCodecSource.getFromProfile(profilePath, tableName);
noBinSource.setFeatureWindowSize(featWindowSize);
binSource.binColName = null;
Iterator<Feature> binFeats = binSource.getFeatures(chr, start, end);
Iterator<Feature> noBinFeats = noBinSource.getFeatures(chr, start, end);
assertNotNull(binFeats);
assertNotNull(noBinFeats);
int count = 0;
while (binFeats.hasNext()) {
assertTrue(noBinFeats.hasNext());
Feature bf = binFeats.next();
Feature nbf = noBinFeats.next();
assertEquals(chr, bf.getChr());
assertTrue(bf.getStart() >= start);
assertTrue(bf.getStart() < end);
assertEquals(nbf.getChr(), bf.getChr());
assertEquals(nbf.getStart(), bf.getStart());
assertEquals(nbf.getEnd(), bf.getEnd());
count++;
}
assertFalse(noBinFeats.hasNext());
}
}