private static void assertEqualList(List<?> a, Collection<?> b) {
if (a.size() == b.size()) {
for (Object x : a) {
if (!b.contains(x))
throw new AssertionFailedError("expected:<" + a + "> but was: <" + b + ">");
}
return;
}
throw new AssertionFailedError("expected:<" + a + "> but was: <" + b + ">");
}
private void processResources(Session session, Element element, HashMap additionalInformation) {
dataFiles = new ArrayList();
missingDataFiles = new ArrayList();
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
if (missingDataFiles.size() > 0) {
StringBuffer message = new StringBuffer();
message.append("<html>The following data file(s) could not be located.<ul>");
for (ResourceLocator file : missingDataFiles) {
if (file.isLocal()) {
message.append("<li>");
message.append(file.getPath());
message.append("</li>");
} else {
message.append("<li>Server: ");
message.append(file.getServerURL());
message.append(" Path: ");
message.append(file.getPath());
message.append("</li>");
}
}
message.append("</ul>");
message.append("Common reasons for this include: ");
message.append("<ul><li>The session or data files have been moved.</li> ");
message.append(
"<li>The data files are located on a drive that is not currently accessible.</li></ul>");
message.append("</html>");
MessageUtils.showMessage(message.toString());
}
if (dataFiles.size() > 0) {
final List<String> errors = new ArrayList<String>();
// Load files concurrently -- TODO, put a limit on # of threads?
List<Thread> threads = new ArrayList(dataFiles.size());
long t0 = System.currentTimeMillis();
int i = 0;
List<Runnable> synchronousLoads = new ArrayList<Runnable>();
for (final ResourceLocator locator : dataFiles) {
final String suppliedPath = locator.getPath();
final String relPath = fullToRelPathMap.get(suppliedPath);
Runnable runnable =
new Runnable() {
public void run() {
List<Track> tracks = null;
try {
tracks = igv.load(locator);
for (Track track : tracks) {
if (track == null) {
log.info("Null track for resource " + locator.getPath());
continue;
}
String id = track.getId();
if (id == null) {
log.info("Null track id for resource " + locator.getPath());
continue;
}
if (relPath != null) {
id = id.replace(suppliedPath, relPath);
}
List<Track> trackList = trackDictionary.get(id);
if (trackList == null) {
trackList = new ArrayList();
trackDictionary.put(id, trackList);
}
trackList.add(track);
}
} 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);
}
}
};
boolean isAlignment =
locator.getPath().endsWith(".bam")
|| locator.getPath().endsWith(".entries")
|| locator.getPath().endsWith(".sam");
// Run synchronously if in batch mode or if there are no "track" elments, or if this is an
// alignment file
if (isAlignment || Globals.isBatch() || !hasTrackElments) {
synchronousLoads.add(runnable);
} else {
Thread t = new Thread(runnable);
threads.add(t);
t.start();
}
i++;
}
// Wait for all threads to complete
for (Thread t : threads) {
try {
t.join();
} catch (InterruptedException ignore) {
}
}
// Now load data that must be loaded synchronously
for (Runnable runnable : synchronousLoads) {
runnable.run();
}
long dt = System.currentTimeMillis() - t0;
log.debug("Total load time = " + dt);
if (errors.size() > 0) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Errors were encountered loading the session:<br>");
for (String msg : errors) {
buf.append(msg);
}
MessageUtils.showMessage(buf.toString());
}
}
dataFiles = null;
}