/*
* 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.
*/
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package org.broad.igv.feature.genome;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.DirectoryManager;
import org.broad.igv.PreferenceManager;
import org.broad.igv.util.FileUtils;
import org.broad.igv.util.RunnableResult;
import org.broad.igv.util.TestUtils;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.net.URL;
import static org.junit.Assert.*;
/**
* @author jrobinso
*/
public class GenomeManagerTest extends AbstractHeadlessTest {
static GenomeManager genomeManager;
public GenomeManagerTest() {
}
@BeforeClass
public static void setUpClass() throws Exception {
GenomeManager.getInstance().clearGenomeCache();
AbstractHeadlessTest.setUpClass();
genomeManager = GenomeManager.getInstance();
}
@Test
public void testGenerateGenomeList() throws Exception {
File inDir = new File(TestUtils.DATA_DIR, "genomes");
String outPath = TestUtils.TMP_OUTPUT_DIR + "/genomelist.txt";
String rootPath = "http://igvdata.broadinstitute.org/genomes";
genomeManager.generateGenomeList(inDir, rootPath, outPath);
BufferedReader reader = new BufferedReader(new FileReader(outPath));
int count = 0;
String line;
while ((line = reader.readLine()) != null) {
assertTrue(line.contains(rootPath + "/"));
count++;
}
assertEquals(6, count);
}
private String genomeZipFile = TestUtils.TMP_OUTPUT_DIR + "tmp.genome";
private String fastaFileRelPath = TestUtils.DATA_DIR + "fasta/ecoli_out.padded.fasta";
private String genomeDisplayName = "Unit test genome";
private String genomeId = "gmt_001";
private void createDotGenomeForTest(String fastaFileName) throws IOException{
GenomeManager.getInstance().getUserDefinedGenomeArchiveList();
GenomeListItem genomeListItem = GenomeManager.getInstance().defineGenome(
new File(genomeZipFile), null, null,
fastaFileName, null, genomeDisplayName,
genomeId, null);
}
/**
* Use a relative path for fasta file, test that we can load it
* @throws Exception
*/
@Test
public void testLoadGenomeFastaRelative() throws Exception{
createDotGenomeForTest(fastaFileRelPath);
Genome relGenome = GenomeManager.getInstance().loadGenome(genomeZipFile, null);
checkGenome(relGenome);
}
/**
* Use an absolute path for fasta file, test that we can load it
* @throws Exception
*/
@Test
public void testLoadGenomeFastaAbsolute() throws Exception{
File fastaFile = new File(fastaFileRelPath);
String fastaAbsPath = fastaFile.getAbsolutePath();
createDotGenomeForTest(fastaAbsPath);
Genome absGenome = GenomeManager.getInstance().loadGenome(genomeZipFile, null);
checkGenome(absGenome);
}
private void checkGenome(Genome genome) {
String chr = genome.getAllChromosomeNames().get(0);
int end = 10;
byte[] seq = genome.getSequence(chr, 0, end);
assertNotNull(seq);
assertEquals(end, seq.length);
}
@Test
public void testLoadFastaOrdering() throws Exception{
String fastaPath = TestUtils.DATA_DIR + "fasta/out_order.fa";
TestUtils.createIndex(fastaPath);
Genome genome = GenomeManager.getInstance().loadGenome(fastaPath, null);
String[] chromos = {"chr5", "chr1"};
assertArrayEquals(chromos, genome.getAllChromosomeNames().toArray());
}
/**
* Test defining a genome from a chrom.sizes file
*
* @throws Exception
*/
@Test
public void testLoadChromSizes() throws Exception {
String testFile = TestUtils.DATA_DIR + "genomes/hg19.chrom.sizes";
Genome genome = GenomeManager.getInstance().loadGenome(testFile, null);
assertEquals(24, genome.getAllChromosomeNames().size());
assertEquals(3095677412l, genome.getTotalLength());
}
/**
* Test for simple downloading of .genome file,
* which packages up all the resources it can
* @throws Exception
*/
@Test
public void testDownloadDotGenome() throws Exception{
String genId = "NC_001802";
String genomePath = "http://igv.broadinstitute.org/genomes/" + genId + ".genome";
String outDirPath = TestUtils.TMP_OUTPUT_DIR;
File outDirFile = new File(outDirPath);
File outGenomeFile = new File(outDirPath, genId + ".genome");
RunnableResult result = GenomeManager.getInstance().downloadWholeGenome(genomePath, outDirFile, null);
assertTrue("Download of genome failed", result.isSuccess());
assertTrue(outGenomeFile.exists());
File fastaFile = new File(TestUtils.TMP_OUTPUT_DIR, genId + ".fna");
assertTrue("fasta file not found: " + fastaFile.getAbsolutePath(), fastaFile.exists());
//I don't know exactly why this is necessary but it seems like there is some weird memory-buffering issue
//and if we try to read from the outPath again it uses the old (remote) fasta file name.
//This is just a unit test thing, copying the downloaded .genome file should have the same info
//and it makes the tests pass
File tmpOut = new File(TestUtils.TMP_OUTPUT_DIR + "t2.genome");
FileUtils.copyFile(outGenomeFile, tmpOut);
GenomeDescriptor descriptor = GenomeManager.parseGenomeArchiveFile(tmpOut);
assertEquals(fastaFile.getAbsolutePath(), descriptor.getSequenceLocation());
assertTrue(descriptor.hasCustomSequenceLocation());
String remSequencePath = "http://igvdata.broadinstitute.org/genomes/seq/Human_immunodeficiency_virus_1_uid15476/NC_001802.fna";
FastaIndexedSequence remSequence = new FastaIndexedSequence(remSequencePath);
TestUtils.createIndex(fastaFile.getAbsolutePath());
FastaIndexedSequence localSequence = new FastaIndexedSequence(fastaFile.getAbsolutePath());
assertEquals(remSequence.getChromosomeNames(), localSequence.getChromosomeNames());
}
@Test
public void testRewriteSequenceLocation() throws Exception{
String origGenomePath = TestUtils.DATA_DIR + "genomes/hg18.unittest.genome";
File newGenomeFile = File.createTempFile("hg18.unittest.testrewrite", ".genome");
FileUtils.copyFile(new File(origGenomePath), newGenomeFile);
newGenomeFile.deleteOnExit();
String newSeqLocation = (new File(TestUtils.TMP_OUTPUT_DIR + "/myseq.fa")).getAbsolutePath();
boolean success = GenomeManager.rewriteSequenceLocation(newGenomeFile, newSeqLocation);
assertTrue("Rewrite of .genome failed", success);
GenomeDescriptor descriptor = GenomeManager.parseGenomeArchiveFile(newGenomeFile);
assertEquals(newSeqLocation, descriptor.getSequenceLocation());
assertTrue(descriptor.hasCustomSequenceLocation());
}
@Test
public void testLoadNonCustomGenome() throws Exception{
String genomePath = TestUtils.DATA_DIR + "genomes/hg18.unittest.genome";
GenomeDescriptor descriptor = GenomeManager.parseGenomeArchiveFile(new File(genomePath));
assertFalse(descriptor.hasCustomSequenceLocation());
}
/**
* Test that when we update a cached genome with custom sequence, the sequence location is preserved
* We have 2 .genome files in the test directory which are very similar.
* We copy one to the genome cache directory and rewrite the sequence
* Then we download the other (needs to be remote)
* We then check that the rewritten sequence was preserved, and differing properties were updated
* @throws Exception
*/
@Test
public void testRefreshCacheLocalSequence() throws Exception{
String cachedSrcPath = TestUtils.DATA_DIR + "genomes/local.unittest_cached.genome";
File cachedSrcFile = new File(cachedSrcPath);
File cachedFile = new File(DirectoryManager.getGenomeCacheDirectory(), cachedSrcFile.getName());
FileUtils.copyFile(cachedSrcFile, cachedFile);
//The local variable names "updatedDescriptor" and "newDescriptor" are somewhat
//confusing, but I don't know how to do better
File updatedFile = new File(TestUtils.DATA_DIR + "genomes/local.unittest_updated.genome");
GenomeDescriptor updatedDescriptor = GenomeManager.parseGenomeArchiveFile(updatedFile);
GenomeDescriptor cachedDescriptor = GenomeManager.parseGenomeArchiveFile(cachedFile);
String targetSeqLocation = cachedDescriptor.getSequenceLocation();
assert (cachedDescriptor.hasCustomSequenceLocation());
//TODO We could point to github instead of the Broad, only real benefit is if we ever change
//this file it's one less manual update step
//String parent = "https://github.com/broadinstitute/IGV/tree/master/test/data/genomes";
String parent = "http://www.broadinstitute.org/igvdata/test";
URL remURL = new URL(parent + "/" + updatedFile.getName());
PreferenceManager.getInstance().put(PreferenceManager.AUTO_UPDATE_GENOMES, true);
GenomeManager.getInstance().refreshCache(cachedFile, remURL);
GenomeDescriptor newDescriptor = GenomeManager.parseGenomeArchiveFile(cachedFile);
assertEquals(targetSeqLocation, newDescriptor.getSequenceLocation());
assertTrue(newDescriptor.hasCustomSequenceLocation());
assertEquals(updatedDescriptor.getName(), newDescriptor.getName());
assertEquals(updatedDescriptor.getGeneFileName(), newDescriptor.getGeneFileName());
assertNotSame(newDescriptor.getName(), cachedDescriptor.getName());
}
}