/**
* Generate the list of files and make them into FileSplits. This needs to be copied to insert a
* filter on acceptable data
*/
@Override
public List<InputSplit> getSplits(JobContext job) throws IOException {
long minSize = Math.max(getFormatMinSplitSize(), getMinSplitSize(job));
long maxSize = getMaxSplitSize(job);
long desiredMappers =
job.getConfiguration().getLong("org.systemsbiology.jxtandem.DesiredXMLInputMappers", 0);
// generate splits
List<InputSplit> splits = new ArrayList<InputSplit>();
List<FileStatus> fileStatuses = listStatus(job);
boolean forceNumberMappers = fileStatuses.size() == 1;
for (FileStatus file : fileStatuses) {
Path path = file.getPath();
if (!isPathAcceptable(path)) // filter acceptable data
continue;
FileSystem fs = path.getFileSystem(job.getConfiguration());
long length = file.getLen();
BlockLocation[] blkLocations = fs.getFileBlockLocations(file, 0, length);
if ((length != 0) && isSplitable(job, path)) {
long blockSize = file.getBlockSize();
// use desired mappers to force more splits
if (forceNumberMappers && desiredMappers > 0)
maxSize = Math.min(maxSize, (length / desiredMappers));
long splitSize = computeSplitSize(blockSize, minSize, maxSize);
long bytesRemaining = length;
while (withinSlop(splitSize, bytesRemaining)) {
int blkIndex = getBlockIndex(blkLocations, length - bytesRemaining);
splits.add(
new FileSplit(
path, length - bytesRemaining, splitSize, blkLocations[blkIndex].getHosts()));
bytesRemaining -= splitSize;
}
if (bytesRemaining != 0) {
splits.add(
new FileSplit(
path,
length - bytesRemaining,
bytesRemaining,
blkLocations[blkLocations.length - 1].getHosts()));
}
} else if (length != 0) {
splits.add(new FileSplit(path, 0, length, blkLocations[0].getHosts()));
} else {
// Create empty hosts array for zero length files
splits.add(new FileSplit(path, 0, length, new String[0]));
}
}
System.out.println("Total # of splits: " + splits.size());
// LOG.debug("Total # of splits: " + splits.size());
return splits;
}
private FSDataOutputStream create(Path f, Reporter reporter, FileStatus srcstat)
throws IOException {
if (destFileSys.exists(f)) {
destFileSys.delete(f, false);
}
if (!preserve_status) {
return destFileSys.create(f, true, sizeBuf, reporter);
}
FsPermission permission =
preseved.contains(FileAttribute.PERMISSION) ? srcstat.getPermission() : null;
short replication =
preseved.contains(FileAttribute.REPLICATION)
? srcstat.getReplication()
: destFileSys.getDefaultReplication();
long blockSize =
preseved.contains(FileAttribute.BLOCK_SIZE)
? srcstat.getBlockSize()
: destFileSys.getDefaultBlockSize();
return destFileSys.create(f, permission, true, sizeBuf, replication, blockSize, reporter);
}