/*
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*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
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* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
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*
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.batch;
import org.apache.commons.lang.StringUtils;
import org.broad.igv.Globals;
import org.broad.igv.prefs.Constants;
import org.broad.igv.dev.api.batch.Command;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.track.RegionScoreType;
import org.broad.igv.track.Track;
import org.broad.igv.ui.AbstractHeadedTest;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestRule;
import org.junit.rules.Timeout;
import javax.imageio.ImageIO;
import java.awt.*;
import java.awt.image.BufferedImage;
import java.io.File;
import java.util.*;
import java.util.List;
import static junit.framework.Assert.*;
import static org.junit.Assert.assertTrue;
/**
* User: jacob
* Date: 2012/03/21
*/
public class CommandExecutorTest extends AbstractHeadedTest {
CommandExecutor exec = new CommandExecutor();
private final String snapshotDir = TestUtils.TMP_OUTPUT_DIR;
@Rule
public TestRule testTimeout = new Timeout((int) 1800000);
public static int checkIsSorted(List<Track> tracks, RegionOfInterest roi, RegionScoreType type, int zoom, ReferenceFrame frame) {
String chr = roi.getChr();
int start = roi.getStart();
int end = roi.getEnd();
String frameName = frame != null ? frame.getName() : null;
Track lastTrack = null;
int count = 0;
for (int ii = 0; ii < tracks.size(); ii++) {
Track track = tracks.get(ii);
if (track.isRegionScoreType(type)) {
String name = track.getName().toLowerCase();
if (name.contains("reference")
|| name.contains("refseq")) {
continue;
}
count++;
if (lastTrack == null) {
lastTrack = track;
continue;
}
// Test sort order -- by default tracks should be sorted in descending value
float s2 = track.getRegionScore(chr, start, end, zoom, type, frameName);
float s1 = lastTrack.getRegionScore(chr, start, end, zoom, type, frameName);
assertTrue("Track named " + track.getName() + ", " + s2 + " and " + lastTrack.getName() + ", " + s1 + " out of order type " + type, s2 <= s1);
lastTrack = track;
}
}
return count;
}
@Before
public void setUp() throws Exception {
super.setUp();
Globals.setBatch(true);
GenomeManager.getInstance().loadGenome(TestUtils.defaultGenome, null);
igv.newSession();
exec.setSnapshotDirectory(snapshotDir);
}
@Test
public void testRegionNoname() throws Exception {
tstRegion(null);
}
@Test
public void testRegionName() throws Exception {
tstRegion("myregion");
}
public void tstRegion(String desc) throws Exception {
String regionStr = "chr1:50-1000";
String descstr = desc != null ? desc : "";
exec.execute("region " + regionStr + " " + descstr);
Collection<RegionOfInterest> regions = IGV.getInstance().getSession().getAllRegionsOfInterest();
assertEquals(1, regions.size());
ArrayList<RegionOfInterest> regionsAL = (ArrayList<RegionOfInterest>) regions;
RegionOfInterest region = regionsAL.get(0);
assertEquals("chr1", region.getChr());
assertEquals(49, region.getStart());
assertEquals(1000, region.getEnd());
assertEquals(descstr, region.getDescription());
}
@Test
@Ignore
public void stressTestSnapshotsHG00171() throws Exception {
PreferencesManager.getPreferences().put(Constants.SAM_MAX_VISIBLE_RANGE, "1000");
String interv0 = "chr1:151666000-152666000";
String interv1 = "chr1:154666000-155666000";
String[] intervals = {interv0, interv1};
String filePath = TestUtils.LARGE_DATA_DIR + "HG00171.hg18.bam";
stressTstSnapshots(filePath, intervals);
}
@Test
@Ignore
public void stressTestSnapshotsBodymap() throws Exception {
PreferencesManager.getPreferences().put(Constants.SAM_DOWNSAMPLE_READS, "true");
PreferencesManager.getPreferences().put(Constants.SAM_SAMPLING_COUNT, "100");
PreferencesManager.getPreferences().put(Constants.SAM_MAX_VISIBLE_RANGE, "1000");
String interv0 = "chr12:97,509,534-97,521,909"; //SLC25A3
String interv1 = "chrX:153,366,844-153,374,196"; //SLC10A3
String[] intervals = {interv0, interv1};
String filePath = TestUtils.DATA_DIR + "sessions/bodymap_3tissue.xml";
stressTstSnapshots(filePath, intervals);
}
/**
* Take a large number of snapshots, make sure they all
* actually show data.
*
* @throws Exception
*/
public void stressTstSnapshots(String filePath, String[] intervals) throws Exception {
exec.execute("load " + filePath);
//exec.execute(("setSleepInterval 10000"));
//For each interval we base our expected size on the first snapshot
Map<String, Long> intervalSizeMap = new HashMap<String, Long>(intervals.length);
Long expSize;
long margin;
int numTrials = 50;
for (int tri = 0; tri < numTrials; tri++) {
int intInd = tri % intervals.length;
String interval = intervals[intInd];
expSize = intervalSizeMap.get(interval);
exec.execute("goto " + interval);
String outFileName = outFileBase + tri + ".png";
File outFile = new File(snapshotDir, outFileName);
if (outFile.exists()) outFile.delete();
tstSnapshot(outFileName);
long size = outFile.length();
if (expSize == null) {
expSize = size;
intervalSizeMap.put(interval, expSize);
}
margin = expSize / 10;
long sizeDiff = Math.abs(size - expSize);
//break;
assertTrue(String.format("File size much different than expected. Trial %d, Diff = %d, margin = %d", tri, sizeDiff, margin), sizeDiff < margin);
}
}
@Test
public void testSetMaxDepth() throws Exception {
setCheckMaxDepth(5);
setCheckMaxDepth(50);
}
private void setCheckMaxDepth(int maxDepth) {
String res = exec.execute("maxDepth " + maxDepth);
assertFalse(res.contains("ERROR"));
int newMaxDepth = PreferencesManager.getPreferences().getAsInt(Constants.SAM_SAMPLING_COUNT);
assertEquals(maxDepth, newMaxDepth);
}
@Test
public void testSortByRegionScoreType() throws Exception {
Timer deadlockChecker = TestUtils.startDeadlockChecker(1000);
String sessionPath = TestUtils.DATA_DIR + "sessions/metabric_expression.xml";
TestUtils.loadSession(igv, sessionPath);
Collection<RegionOfInterest> rois = igv.getSession().getAllRegionsOfInterest();
List<Track> tracks;
int count = 0;
for (RegionOfInterest roi : rois) {
for (RegionScoreType type : RegionScoreType.values()) {
igv.sortAllTracksByAttributes(new String[]{"NAME"}, new boolean[]{false});
String typeStr = type.toString().toUpperCase();
if (count % 2 == 0) {
typeStr = typeStr.toLowerCase();
}
String resp = exec.execute("sort " + typeStr + " " + roi.getLocusString());
assertEquals("OK", resp);
tracks = igv.getAllTracks();
ReferenceFrame frame = FrameManager.getDefaultFrame();
checkIsSorted(tracks, roi, type, frame.getZoom(), frame);
count++;
}
}
deadlockChecker.cancel();
deadlockChecker.purge();
}
private final String outFileBase = "testSnap";
@Test
public void testSnapShotPng() throws Exception {
String outFileName = outFileBase + ".Png";
tstSnapshot(outFileName);
}
@Test
public void testSnapshotTracksOnly() throws Exception {
String outFileName = outFileBase + "_track.png";
tstSnapshot(outFileName, true, "trackpanels");
}
@Test
public void testSnapShotJpeg() throws Exception {
tstSnapshot(outFileBase + ".jpeg");
}
@Test
public void testSnapShotJpg() throws Exception {
tstSnapshot(outFileBase + ".jpg");
}
@Test
public void testSnapShotSvg() throws Exception {
String outFileName = outFileBase + ".svG";
tstSnapshot(outFileName);
}
@Test
public void testSnapShotFails() throws Exception {
String[] exts = new String[]{"abc", "svt", "pnq"};
for (String ext : exts) {
String outFileName = outFileBase + "." + ext;
tstSnapshot(outFileName, false, null);
}
}
public File tstSnapshot(String outFileName) throws Exception {
return tstSnapshot(outFileName, true, null);
}
public File tstSnapshot(String outFileName, boolean shouldSucceed, String moreargs) throws Exception {
File out = new File(snapshotDir, outFileName);
assertFalse(out.exists());
String toexec = "snapshot " + outFileName;
if (moreargs != null && moreargs.length() > 0) {
toexec += " " + moreargs;
}
exec.execute(toexec);
assertEquals(shouldSucceed, out.exists());
return out;
}
public static final String urlPathSpaces = "ftp://ftp.broadinstitute.org/distribution/igv/TEST/cpgIslands%20with%20spaces.hg18.bed";
public static final String dirPathSpaces = TestUtils.DATA_DIR + "folder with spaces";
public static final String fileName01 = "test.wig";
public static final String fileNamePerc = "%test%2D.wig";
public static final String fileNamePlus = "test+wp.wig";
public static final String fileNameCommas = "test,with,commas.wig";
@Test
public void testLoadFileSpaces() throws Exception {
tstLoadFileSpaces(fileName01);
}
@Test
public void testLoadFileSpacesPerc() throws Exception {
tstLoadFileSpaces(fileNamePerc);
}
@Test
public void testLoadFileCommas() throws Exception {
tstLoadFileSpaces(fileNameCommas);
}
@Test
public void testLoadFileSpacesPlus() throws Exception {
tstLoadFileSpaces(fileNamePlus);
}
@Test
public void testLoadFileURLSpaces() throws Exception {
tstLoadFileURLSpaces(fileName01);
}
@Test
public void testLoadFileURLSpacesPerc() throws Exception {
tstLoadFileURLSpaces(fileNamePerc);
}
@Test
public void testLoadFileURLSpacesPlus() throws Exception {
tstLoadFileURLSpaces(fileNamePlus);
}
@Test
public void testLoadFileURLCommas() throws Exception {
tstLoadFileURLSpaces(fileNameCommas);
}
private void tstLoadFileURLSpaces(String filename) throws Exception {
String fileURL = "file://" + org.broad.igv.util.StringUtils.encodeURL(new File(dirPathSpaces, filename).getAbsolutePath());
exec.execute("load \"" + fileURL + "\"");
TestUtils.assertTrackLoaded(IGV.getInstance(), filename);
}
private void tstLoadFileSpaces(String filename) throws Exception {
File file = new File(dirPathSpaces, filename);
exec.execute("load \"" + file.getPath() + "\"");
TestUtils.assertTrackLoaded(IGV.getInstance(), filename);
}
@Test
public void testLoadURL() throws Exception {
//This is mostly to ruggedize test setup. The setup may load
//reference/sequence tracks, we'd like to be able to change
//test setup and not worry about this test.
int beginTracks = igv.getAllTracks().size();
String urlPath = urlPathSpaces;
Map<String, String> params = null;
String name = "hasSpaces";
String format = "bed";
String index = null;
String coverage = null;
String locus = null;
boolean merge = true;
exec.loadFiles(urlPath, index, coverage, name, format, locus, merge, params);
name = null;
String localPath = TestUtils.DATA_DIR + "bed/test.bed";
exec.loadFiles(localPath, index, coverage, name, format, locus, merge, params);
assertEquals(2, igv.getAllTracks().size() - beginTracks);
}
@Test
public void testSetDataRange() throws Exception {
String dataFile = TestUtils.DATA_DIR + "igv/recombRate.ens.igv.txt";
Map<String, String> params = null;
String name = null;
String format = null;
String index = null;
String coverage = null;
String locus = null;
boolean merge = true;
exec.loadFiles(dataFile, index, coverage, name, format, locus, merge, params);
String[] goodArgSet = new String[]{"0,5.0 ", "0,1,5", "-1,0,1", "-1.32,10.21"};
for (String arg : goodArgSet) {
String resp = exec.execute("setDataRange " + arg);
assertEquals("OK", resp);
}
String[] badArgSet = new String[]{"0 ", "-1,0,2,3", "o,1o"};
for (String arg : badArgSet) {
String resp = exec.execute("setDataRange " + arg);
assertTrue(resp.toLowerCase().startsWith("error"));
}
}
@Test
public void testLoadGenomesById() throws Exception {
String[] genomeIds = new String[]{"hg19", "mm10", "rn5", "canFam2", "bosTau7", "sacCer3", "WS220"};
for (String genomeId : genomeIds) {
String result = exec.execute("genome " + genomeId);
assertEquals("OK", result);
assertEquals(genomeId, GenomeManager.getInstance().getCurrentGenome().getId());
}
}
@Test
public void testLoadGenomeFile() throws Exception {
String[] genomePaths = new String[]{TestUtils.DATA_DIR + "genomes/hg18.unittest.genome"};
String[] genomeIds = new String[]{"hg18.unittest"};
int ind = 0;
for (String genomePath : genomePaths) {
String result = exec.execute("genome " + genomePath);
assertEquals("OK", result);
assertEquals(genomeIds[ind++], GenomeManager.getInstance().getCurrentGenome().getId());
}
}
@Test
public void testLoadGenomeFastaFile() throws Exception {
String[] genomePaths = new String[]{TestUtils.DATA_DIR + "fasta/ecoli_out.padded.fasta"};
String[] genomeIds = genomePaths;
int ind = 0;
for (String genomePath : genomePaths) {
String result = exec.execute("genome " + genomePath);
assertEquals("OK", result);
assertEquals(genomeIds[ind++], GenomeManager.getInstance().getCurrentGenome().getId());
}
}
@Test
public void testLoadGenomesFail() throws Exception {
String startId = genome.getId();
String[] genomeIds = new String[]{"hg1920", "inch10", "doctor5"};
for (String genomeId : genomeIds) {
String result = exec.execute("genome " + genomeId);
assertTrue(result.toLowerCase().startsWith(("error")));
assertEquals(startId, GenomeManager.getInstance().getCurrentGenome().getId());
}
}
@Test
public void testLoadIndex() throws Exception {
String urlPath = TestUtils.DATA_DIR + "bam/NA12878.SLX.sample.bam";
String index = TestUtils.DATA_DIR + "bam/NA12878.SLX.sample.bam.bai";
String name = null;
String format = "bam";
String coverage = null;
String locus = "chr1:155,156,300-155,164,706"; //muc1
boolean merge = true;
Map<String, String> params = null;
exec.loadFiles(urlPath, index, coverage, name, format, locus, merge, params);
List<Track> tracks = igv.getAllTracks();
// Find our alignment track
boolean foundTrack = false;
for(Track t : tracks) {
ResourceLocator rl = t.getResourceLocator();
if(rl != null && rl.getPath().equals(urlPath)) {
foundTrack = true;
}
}
assertTrue(foundTrack);
}
@Test
public void testPreference() throws Exception {
String key = Constants.DATA_SERVER_URL_KEY;
String val = "myDataServerURL";
assertNotSame(val, PreferencesManager.getPreferences().getDataServerURL());
exec.execute(String.format("preference %s %s", key, val));
assertEquals(val, PreferencesManager.getPreferences().getDataServerURL());
}
@Test
public void testSnapshotsize() throws Exception {
String filePath = TestUtils.DATA_DIR + "bam/NA12878.SLX.sample.bam";
int numLoads = 1;
for (int ii = 0; ii < numLoads; ii++) {
IGV.getInstance().loadResources(Arrays.asList(new ResourceLocator(filePath)));
}
exec.execute("goto chr1:9,713,386-9,733,865");
int minHeight = (int) Toolkit.getDefaultToolkit().getScreenSize().getHeight() - 150;
int maxHeight = minHeight + 200;
String outFileName = minHeight + ".png";
exec.execute("maxpanelheight " + maxHeight);
exec.execute("snapshot " + outFileName);
File outputFile = new File(snapshotDir, outFileName);
BufferedImage image = ImageIO.read(outputFile);
assertTrue("Output image height " + image.getHeight() + " is not at least " + minHeight, image.getHeight() > minHeight);
int remAlphaMask = 0x00ffffff;
int numBlackPix = 0;
for (int yy = image.getMinY(); yy < image.getHeight(); yy++) {
for (int xx = image.getMinX(); xx < image.getWidth(); xx++) {
int color = image.getRGB(xx, yy) & remAlphaMask;
numBlackPix += color == 0 ? 1 : 0;
}
}
//Just making sure we don't trivially satisfy the problem
assertTrue(numBlackPix > 100);
int totalPix = image.getHeight() * image.getWidth();
assertTrue("Too much of the snapshot is black", numBlackPix < totalPix * 0.1);
}
@Test
public void testCustomCommand_Echo() throws Exception {
String cmd = EchoCommand.class.getName();
String otherArgs = "fly high free bird";
String fullCmd = String.format("%s %s", cmd, otherArgs);
String response = exec.execute(fullCmd);
assertEquals(otherArgs, response);
}
public static class EchoCommand implements Command {
@Override
public String run(List<String> args) {
return StringUtils.join(args, " ");
}
}
}