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A Java API for high-throughput sequencing data (HTS) formats
/*
* The MIT License
*
* Copyright (c) 2014 The 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 htsjdk.samtools.util;
import htsjdk.samtools.Defaults;
import htsjdk.samtools.SAMException;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayDeque;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.Queue;
import java.util.stream.Collectors;
/**
* A single-ended FIFO queue. Writes elements to temporary files when the queue gets too big.
* External references to elements in this queue are NOT guaranteed to be valid, due to the disk write/read
*
* NB: The queue becomes read-only after the first time that an on-disk record is "next up" to be read (i.e. has been
* loaded into headRecord). Max size is therefore non-deterministic.
* This avoids issues arising from conflicts between the input and output streams.
* This could perhaps be avoided by creating a version of BAMRecordCodec that operates on RandomAccessFiles or channels.
*
*
*
* Created by bradt on 4/28/14.
*/
public class DiskBackedQueue implements Queue {
private final int maxRecordsInRamQueue;
private final Queue ramRecords;
private Path diskRecords = null;
private final TempStreamFactory tempStreamFactory = new TempStreamFactory();
private OutputStream outputStream = null;
private InputStream inputStream = null;
private boolean canAdd = true;
private int numRecordsOnDisk = 0;
/** Record representing the head of the queue; returned by peek, poll **/
private E headRecord = null;
/** Directories where file of records go. **/
private final List tmpDirs;
/**
* Used to write records to file, and used as a prototype to create codecs for reading.
*/
private final SortingCollection.Codec codec;
/**
* Prepare to accumulate records
*
* @param codec For writing records to file and reading them back into RAM
* @param maxRecordsInRam how many records to accumulate before spilling to disk
* @param tmpDirs Where to write files of records that will not fit in RAM
*/
private DiskBackedQueue(final SortingCollection.Codec codec,
final int maxRecordsInRam, final List tmpDirs) {
if (maxRecordsInRam < 0) {
throw new IllegalArgumentException("maxRecordsInRamQueue must be >= 0");
}
if (tmpDirs == null || tmpDirs.isEmpty()) {
throw new IllegalArgumentException("At least one temp directory must be provided.");
}
for (final Path tmpDir : tmpDirs) IOUtil.assertDirectoryIsWritable(tmpDir);
this.tmpDirs = tmpDirs;
this.codec = codec;
this.maxRecordsInRamQueue = (maxRecordsInRam == 0) ? 0 : maxRecordsInRam - 1; // the first of our ram records is stored as headRecord
this.ramRecords = new ArrayDeque(this.maxRecordsInRamQueue);
}
/**
* Syntactic sugar around the ctor, to save some typing of type parameters
*
* @param codec For writing records to file and reading them back into RAM
* @param maxRecordsInRam how many records to accumulate in memory before spilling to disk
* @param tmpDir Where to write files of records that will not fit in RAM
*/
public static DiskBackedQueue newInstance(final SortingCollection.Codec codec,
final int maxRecordsInRam,
final List tmpDir) {
return new DiskBackedQueue(codec, maxRecordsInRam, tmpDir.stream().map(File::toPath).collect(Collectors.toList()));
}
/**
* Syntactic sugar around the ctor, to save some typing of type parameters
*
* @param codec For writing records to file and reading them back into RAM
* @param maxRecordsInRam how many records to accumulate in memory before spilling to disk
* @param tmpDir Where to write files of records that will not fit in RAM
*/
public static DiskBackedQueue newInstanceFromPaths(final SortingCollection.Codec codec,
final int maxRecordsInRam,
final List tmpDir) {
return new DiskBackedQueue(codec, maxRecordsInRam, tmpDir);
}
public boolean canAdd() {
return this.canAdd;
}
public int getNumRecordsOnDisk() {
return this.numRecordsOnDisk;
}
public boolean headRecordIsFromDisk() {
return (!this.canAdd);
}
/**
* Add the record to the tail of the queue, spilling to disk if necessary
* Must check that (canAdd() == true) before calling this method
*
* @param record The record to be added to the queue
* @return true (if add successful)
* @throws IllegalStateException if the queue cannot be added to
*/
@Override
public boolean add(final E record) throws IllegalStateException {
if (!canAdd) throw new IllegalStateException("Cannot add to DiskBackedQueue whose canAdd() method returns false");
// NB: we add all the records before removing them, so we can never have spilled to disk unless all the space for ram records
// have been exhausted.
if (this.headRecord == null) { // this is the first record in the queue
if (0 < this.numRecordsOnDisk) throw new SAMException("Head record was null but we have records on disk. Bug!");
this.headRecord = record;
}
else if (this.ramRecords.size() == this.maxRecordsInRamQueue) {
spillToDisk(record);
}
else {
if (0 < this.numRecordsOnDisk) throw new SAMException("Trying to add records to RAM but there were records on disk. Bug!");
this.ramRecords.add(record);
}
return true;
}
@Override
public boolean offer(final E e) {
return this.canAdd && this.add(e);
}
@Override
public E remove() {
final E element = this.poll();
if (element == null) {
throw new NoSuchElementException("Attempting to remove() from empty DiskBackedQueue");
}
else {
return element;
}
}
@Override
public E poll() {
final E outRecord = this.headRecord;
if (outRecord != null) {
updateQueueHead();
}
return outRecord;
}
@Override
public E element() {
if (this.headRecord != null) {
return this.headRecord;
}
else {
throw new NoSuchElementException("Attempting to element() from empty DiskBackedQueue");
}
}
@Override
public E peek() {
return this.headRecord;
}
/**
* Return the total number of elements in the queue, both in memory and on disk
*/
@Override
public int size() {
return (this.headRecord == null) ? 0 : (1 + this.ramRecords.size() + this.numRecordsOnDisk);
}
@Override
public boolean isEmpty() {
return (this.headRecord == null);
}
/**
* Add all elements from collection c to this DiskBackedQueue
* Must check that (canAdd() == true) before calling this method
*
* @param c the collection of elements to add
* @return true if this collection changed as a result of the call
* @throws IllegalStateException if the queue cannot be added to
*/
@Override
public boolean addAll(final Collection c) {
try {
for (final E element : c) {
this.add(element);
}
return true;
} catch (final IllegalStateException e) {
throw new IllegalStateException("Cannot add to DiskBackedQueue whose canAdd() method returns false", e);
}
}
@Override
public void clear() {
this.headRecord = null;
this.ramRecords.clear();
this.closeIOResources();
this.outputStream = null;
this.inputStream = null;
this.diskRecords = null;
this.canAdd = true;
}
/**
* Clean up disk resources in case clear() has not been explicitly called (as would be preferable)
* Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file
*
* @throws Throwable
*/
@Override
protected void finalize() throws Throwable {
this.closeIOResources();
super.finalize(); // NB: intellij wanted me to do this. Need I? I'm not extending anything
}
/**
* Write the present record to the end of a file representing the tail of the queue.
* @throws RuntimeIOException
*/
private void spillToDisk(final E record) throws RuntimeIOException {
try {
if (this.diskRecords == null) {
this.diskRecords = newTempFile();
this.outputStream = tempStreamFactory.wrapTempOutputStream(Files.newOutputStream(this.diskRecords), Defaults.BUFFER_SIZE);
this.codec.setOutputStream(this.outputStream);
}
this.codec.encode(record);
this.outputStream.flush();
this.numRecordsOnDisk++;
} catch (final IOException e) {
throw new RuntimeIOException("Problem writing temporary file. Try setting TMP_DIR to a file system with lots of space.", e);
}
}
/**
* Creates a new tmp file on one of the available temp filesystems, registers it for deletion
* on JVM exit and then returns it.
*/
private Path newTempFile() throws IOException {
return IOUtil.newTempPath("diskbackedqueue.", ".tmp", this.tmpDirs.toArray(new Path[tmpDirs.size()]), IOUtil.FIVE_GBS);
}
/**
* Update the head of the queue with the next record in memory or on disk.
* Sets headRecord to null if the queue is now empty
*/
private void updateQueueHead() {
if (!this.ramRecords.isEmpty()) {
this.headRecord = this.ramRecords.poll();
if (0 < numRecordsOnDisk) this.canAdd = false;
}
else if (this.diskRecords != null) {
this.headRecord = this.readFileRecord(this.diskRecords);
this.canAdd = false;
}
else {
this.canAdd = true;
this.headRecord = null;
}
}
/**
* Read back a record that had been spilled to disk. Return null if there are no disk records
* Note- if we are reading disk records, we can no longer add additional elements to this DiskBackedQueue
*
* @param file the file to read from
* @return The next element from the head of the file, or null if end-of-file is reached
* @throws RuntimeIOException
*/
private E readFileRecord (final Path file) {
if (this.canAdd) this.canAdd = false; // NB: should this just be an assignment regardless?
// we never wrote a record to disk
if (file == null) {
throw new IllegalStateException("The file to read from was null");
}
try {
if (this.inputStream == null) {
inputStream = Files.newInputStream(file);
this.codec.setInputStream(tempStreamFactory.wrapTempInputStream(inputStream, Defaults.BUFFER_SIZE));
}
final E record = this.codec.decode(); // NB: returns null if end-of-file is reached.
if (record != null) {
numRecordsOnDisk--;
}
return record;
} catch (final IOException e) {
throw new RuntimeIOException("DiskBackedQueue encountered an error reading from a file", e);
}
}
private void closeIOResources() {
CloserUtil.close(this.outputStream);
CloserUtil.close(this.inputStream);
if (this.diskRecords != null) IOUtil.deletePath(this.diskRecords);
}
/**
* Not supported. Cannot access particular elements, as some elements may have been written to disk
*
* @throws UnsupportedOperationException
*/
@Override
public boolean remove(final Object o) {
throw new UnsupportedOperationException("DiskBackedQueue does not support remove(Object o)");
}
/**
* Not supported. Cannot access particular elements, as some elements may have been written to disk
*
* @throws UnsupportedOperationException
*/
@Override
public boolean removeAll(final Collection c) {
throw new UnsupportedOperationException("DiskBackedQueue does not support removeAll(Collection c)");
}
/**
* Not supported. Cannot access particular elements, as some elements may have been written to disk
*
* @throws UnsupportedOperationException
*/
@Override
public boolean retainAll(final Collection c) {
throw new UnsupportedOperationException("DiskBackedQueue does not support retainAll(Collection c)");
}
/**
* Not supported. It is not possible to check for the presence of a particular element,
* as some elements may have been written to disk
*
* @throws UnsupportedOperationException
*/
@Override
public boolean contains(final Object o) {
throw new UnsupportedOperationException("DiskBackedQueue does not support contains(Object o)");
}
/**
* Not supported. It is not possible to check for the presence of a particular element,
* as some elements may have been written to disk
*
* @throws UnsupportedOperationException
*/
@Override
public boolean containsAll(final Collection c) {
throw new UnsupportedOperationException("DiskBackedQueue does not support containsAll(Collection c)");
}
/**
* Not supported at this time
* @throws UnsupportedOperationException
*/
@Override
public Iterator iterator() {
throw new UnsupportedOperationException("DiskBackedQueue does not support iterator()");
}
/**
* Not supported at this time
* @throws UnsupportedOperationException
*/
@Override
public Object[] toArray() {
throw new UnsupportedOperationException("DiskBackedQueue does not support toArray()");
}
/**
* Not supported at this time
* @throws UnsupportedOperationException
*/
@Override
public T1[] toArray(final T1[] a) {
throw new UnsupportedOperationException("DiskBackedQueue does not support toArray(T1[] a)");
}
}
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