/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* 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.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.session;
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.TrackPanel;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Class to parse an index aware session file
*
* @author Brett T. Hannigan
* @date 09/16/2015
*/
public class IndexAwareSessionReader implements SessionReader {
private static Logger log = Logger.getLogger(IndexAwareSessionReader.class);
IGV igv;
public IndexAwareSessionReader(IGV igv) {
this.igv = igv;
}
/**
* Load an inex aware session from the given stream.
*
* @param inputStream
* @param session
* @param sessionPath
* @throws IOException
*/
public void loadSession(InputStream inputStream, Session session, String sessionPath) throws IOException {
BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
String trackLine = null;
String nextLine;
final List<String> errors = new ArrayList<String>();
final HashMap<String, List<Track>> loadedTracks = new HashMap();
List<ResourceLocator> aSync = new ArrayList();
// Index aware sessions do not have means to set genome, or if they do we don't use it
Genome genome = GenomeManager.getInstance().getCurrentGenome();
if (genome != null) {
IGV.getInstance().setGenomeTracks(genome.getGeneTrack());
}
while ((nextLine = reader.readLine()) != null) {
ResourceLocator locator = null;
try {
if (nextLine.startsWith("#")) {
continue;
} else if (nextLine.startsWith("browser")) {
parseBrowserLine(nextLine, session);
} else if (nextLine.startsWith("track")) {
trackLine = nextLine;
String dataURL = getDataURL(trackLine);
if (dataURL != null) {
locator = new ResourceLocator(dataURL);
String indexURL = getIndexURL(trackLine);
if (indexURL != null) {
locator.setIndexPath(indexURL);
}
String coverageURL = getCoverageURL(trackLine);
if (coverageURL != null) {
locator.setCoverage(coverageURL);
}
loadedTracks.put(dataURL, igv.load(locator));
}
} else {
locator = parseResourceLine(nextLine);
}
if (locator != null) {
locator.setTrackLine(trackLine);
// Alignment tracks must be loaded synchronously
if (isAlignmentFile(locator.getPath())) {
TrackPanel panel = igv.getPanelFor(locator);
panel.addTracks(igv.load(locator));
} else {
aSync.add(locator);
}
trackLine = null; // Reset for next time
locator = null;
}
} catch (Exception e) {
log.error("Error loading resource " + locator.getPath(), e);
String ms = "<b>" + locator.getPath() + "</b><br> " + e.toString() + "<br>";
errors.add(ms);
}
}
loadAsynchronous(aSync, loadedTracks, errors);
if (errors.size() > 0) {
displayErrors(errors);
}
}
private void loadAsynchronous(List<ResourceLocator> aSync, final HashMap<String, List<Track>> loadedTracks,
final List<String> errors) {
List<Thread> threads = new ArrayList(aSync.size());
for (final ResourceLocator locator : aSync) {
Runnable runnable = new Runnable() {
public void run() {
// TODO handle errors
try {
loadedTracks.put(locator.getPath(), igv.load(locator));
} catch (Exception e) {
log.error("Error loading resource " + locator.getPath(), e);
String ms = "<b>" + locator.getPath() + "</b><br>&nbs;p " + e.toString() + "<br>";
errors.add(ms);
}
}
};
Thread t = new Thread(runnable);
threads.add(t);
t.start();
}
// Wait for all threads to complete
for (Thread t : threads) {
try {
t.join();
} catch (InterruptedException ignore) {
}
}
placeTracksInPanels(aSync, loadedTracks);
}
private String getDataURL(String nextLine) {
TrackProperties props = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, props);
return props.getDataURL();
}
private String getIndexURL(String nextLine) {
TrackProperties props = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, props);
return props.getIndexURL();
}
private String getCoverageURL(String nextLine) {
TrackProperties props = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, props);
return props.getCoverageURL();
}
private void placeTracksInPanels(List<ResourceLocator> locatorPaths, Map<String, List<Track>> loadedTracks) {
for (ResourceLocator loc : locatorPaths) {
//TrackPanel panel = IGV.getInstance().getPanelFor(new ResourceLocator(path));
// If loading from an index aware session use a single panel
TrackPanel panel = igv.getTrackPanel(IGV.DATA_PANEL_NAME);
String path = loc.getPath();
if (loadedTracks.containsKey(path)) {
panel.addTracks(loadedTracks.get(path));
}
}
}
private boolean isAlignmentFile(String path) {
return path.endsWith(".bam") || path.endsWith(".entries") || path.endsWith(".sam");
}
/**
* Browser lines have 2 or 3 tokens, e.g.
* browser position chr19:11500000-12000000
*
* @param line
*/
private void parseBrowserLine(String line, Session session) {
String[] tokens = line.split("\\s+");
if (tokens.length >= 3 && tokens[1].equals("position")) {
session.setLocus(tokens[2]);
}
}
private ResourceLocator parseResourceLine(String line) {
ResourceLocator locator = null;
String[] tokens = line.split("\\s+");
if (tokens.length == 1) {
locator = new ResourceLocator(tokens[0]);
}
else if (tokens.length >= 2) {
// Might want to do some error checking here on
// making sure file prefixes match and file extensions
// indicate the index comes second.
locator = new ResourceLocator(tokens[0]);
locator.setIndexPath(tokens[1]);
if (tokens.length >= 3) {
locator.setCoverage(tokens[2]);
}
}
return locator;
}
private void displayErrors(List<String> errors) {
StringBuffer buffer = new StringBuffer();
buffer.append("<html>Errors were encountered while loading session:<br>");
for (String e : errors) {
buffer.append(e);
}
MessageUtils.showMessage(buffer.toString());
}
}