// HeapReader.java
// (C) 2008 by Michael Peter Christen; mc@yacy.net, Frankfurt a. M., Germany
// first published 30.12.2008 on http://yacy.net
//
// $LastChangedDate: 2011-05-27 10:24:54 +0200 (Fr, 27. Mai 2011) $
// $LastChangedRevision: 7746 $
// $LastChangedBy: orbiter $
//
// LICENSE
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
package net.yacy.kelondro.blob;
import java.io.BufferedInputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.Iterator;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ExecutionException;
import net.yacy.cora.document.ASCII;
import net.yacy.cora.document.UTF8;
import net.yacy.kelondro.index.HandleMap;
import net.yacy.kelondro.index.RowSpaceExceededException;
import net.yacy.kelondro.io.CachedFileWriter;
import net.yacy.kelondro.io.Writer;
import net.yacy.kelondro.logging.Log;
import net.yacy.kelondro.order.ByteOrder;
import net.yacy.kelondro.order.CloneableIterator;
import net.yacy.kelondro.order.Digest;
import net.yacy.kelondro.order.NaturalOrder;
import net.yacy.kelondro.order.RotateIterator;
import net.yacy.kelondro.util.FileUtils;
import net.yacy.kelondro.util.LookAheadIterator;
import net.yacy.kelondro.util.MemoryControl;
public class HeapReader {
//public final static long keepFreeMem = 20 * 1024 * 1024;
// input values
protected int keylength; // the length of the primary key
protected File heapFile; // the file of the heap
protected final ByteOrder ordering; // the ordering on keys
// computed values
protected Writer file; // a random access to the file
protected HandleMap index; // key/seek relation for used records
protected Gap free; // set of {seek, size} pairs denoting space and position of free records
private File fingerprintFileIdx, fingerprintFileGap; // files with dumped indexes. Will be deleted if file is written
public HeapReader(
final File heapFile,
final int keylength,
final ByteOrder ordering) throws IOException {
this.ordering = ordering;
this.heapFile = heapFile;
this.keylength = keylength;
this.index = null; // will be created as result of initialization process
this.free = null; // will be initialized later depending on existing idx/gap file
this.heapFile.getParentFile().mkdirs();
this.file = new CachedFileWriter(this.heapFile);
// read or initialize the index
fingerprintFileIdx = null;
fingerprintFileGap = null;
if (initIndexReadDump()) {
// verify that everything worked just fine
// pick some elements of the index
Iterator<byte[]> i = this.index.keys(true, null);
int c = 3;
byte[] b, b1 = new byte[index.row().primaryKeyLength];
long pos;
boolean ok = true;
while (i.hasNext() && c-- > 0) {
b = i.next();
pos = this.index.get(b);
file.seek(pos + 4);
file.readFully(b1, 0, b1.length);
if (!this.ordering.equal(b, b1)) {
ok = false;
break;
}
}
if (!ok) {
Log.logWarning("HeapReader", "verification of idx file for " + heapFile.toString() + " failed, re-building index");
initIndexReadFromHeap();
} else {
Log.logInfo("HeapReader", "using a dump of the index of " + heapFile.toString() + ".");
}
} else {
// if we did not have a dump, create a new index
initIndexReadFromHeap();
}
// merge gaps that follow directly
mergeFreeEntries();
// after the initial initialization of the heap, we close the file again
// to make more room to file pointers which may run out if the number
// of file descriptors is too low and the number of files is too high
this.file.close();
// the file will be opened again automatically when the next access to it comes.
}
public long mem() {
return index.mem(); // don't add the memory for free here since then the asserts for memory management don't work
}
public void trim() {
this.index.trim();
}
protected byte[] normalizeKey(byte[] key) {
// check size of key: zero-filled keys are only possible of the ordering is
// an instance of the natural ordering. Base64-orderings cannot use zeros in keys.
assert key.length >= this.keylength || this.ordering instanceof NaturalOrder;
return normalizeKey(key, this.keylength);
}
private static final byte zero = 0;
protected static byte[] normalizeKey(byte[] key, int keylength) {
if (key.length == keylength) return key;
byte[] k = new byte[keylength];
if (key.length < keylength) {
System.arraycopy(key, 0, k, 0, key.length);
for (int i = key.length; i < keylength; i++) k[i] = zero;
} else {
System.arraycopy(key, 0, k, 0, keylength);
}
return k;
}
private boolean initIndexReadDump() {
// look for an index dump and read it if it exist
// if this is successful, return true; otherwise false
String fingerprint = fingerprintFileHash(this.heapFile);
if (fingerprint == null) {
Log.logSevere("HeapReader", "cannot generate a fingerprint for " + this.heapFile + ": null");
return false;
}
this.fingerprintFileIdx = HeapWriter.fingerprintIndexFile(this.heapFile, fingerprint);
if (!this.fingerprintFileIdx.exists()) this.fingerprintFileIdx = new File(this.fingerprintFileIdx.getAbsolutePath() + ".gz");
this.fingerprintFileGap = HeapWriter.fingerprintGapFile(this.heapFile, fingerprint);
if (!this.fingerprintFileGap.exists()) this.fingerprintFileGap = new File(this.fingerprintFileGap.getAbsolutePath() + ".gz");
if (!this.fingerprintFileIdx.exists() || !this.fingerprintFileGap.exists()) {
deleteAllFingerprints(this.heapFile, this.fingerprintFileIdx.getName(), this.fingerprintFileGap.getName());
return false;
}
// there is an index and a gap file:
// read the index file:
try {
this.index = new HandleMap(this.keylength, this.ordering, 8, this.fingerprintFileIdx);
} catch (IOException e) {
Log.logException(e);
return false;
} catch (RowSpaceExceededException e) {
Log.logException(e);
return false;
}
// check saturation
int[] saturation = this.index.saturation();
Log.logInfo("HeapReader", "saturation of " + this.fingerprintFileIdx.getName() + ": keylength = " + saturation[0] + ", vallength = " + saturation[1] + ", possible saving: " + ((this.keylength - saturation[0] + 8 - saturation[1]) * index.size() / 1024 / 1024) + " MB");
// read the gap file:
try {
this.free = new Gap(this.fingerprintFileGap);
} catch (IOException e) {
Log.logException(e);
return false;
}
// everything is fine now
return !this.index.isEmpty();
}
/**
* deletion of the fingerprint: this should happen if the heap is written or entries are deleted
* if the files are not deleted then it may be possible that they are not used anyway because the
* fingerprint hash does not fit with the heap dump file hash. But since the hash is not computed
* from all the data and just some key bytes it may be possible that the hash did not change.
*/
public void deleteFingerprint() {
if (this.fingerprintFileIdx != null) {
FileUtils.deletedelete(this.fingerprintFileIdx);
this.fingerprintFileIdx = null;
}
if (this.fingerprintFileGap != null) {
FileUtils.deletedelete(this.fingerprintFileGap);
this.fingerprintFileGap = null;
}
}
protected static String fingerprintFileHash(File f) {
assert f != null;
assert f.exists() : "file = " + f.toString();
String fp = Digest.fastFingerprintB64(f, false);
assert fp != null : "file = " + f.toString();
if (fp == null) return null;
return fp.substring(0, 12);
}
private static void deleteAllFingerprints(File f, String exception1, String exception2) {
File d = f.getParentFile();
String n = f.getName();
String[] l = d.list();
for (int i = 0; i < l.length; i++) {
if (!l[i].startsWith(n)) continue;
if (exception1 != null && l[i].equals(exception1)) continue;
if (exception2 != null && l[i].equals(exception2)) continue;
if (l[i].endsWith(".idx") ||
l[i].endsWith(".gap") ||
l[i].endsWith(".idx.gz") ||
l[i].endsWith(".gap.gz")
) FileUtils.deletedelete(new File(d, l[i]));
}
}
private void initIndexReadFromHeap() throws IOException {
// this initializes the this.index object by reading positions from the heap file
Log.logInfo("HeapReader", "generating index for " + heapFile.toString() + ", " + (file.length() / 1024 / 1024) + " MB. Please wait.");
this.free = new Gap();
HandleMap.initDataConsumer indexready = HandleMap.asynchronusInitializer(this.name() + ".initializer", keylength, this.ordering, 8, Math.max(10, (int) (Runtime.getRuntime().freeMemory() / (10 * 1024 * 1024))));
byte[] key = new byte[keylength];
int reclen;
long seek = 0;
loop: while (true) { // don't test available() here because this does not work for files > 2GB
try {
// go to seek position
file.seek(seek);
// read length of the following record without the length of the record size bytes
reclen = file.readInt();
//assert reclen > 0 : " reclen == 0 at seek pos " + seek;
if (reclen == 0) {
// very bad file inconsistency
Log.logSevere("HeapReader", "reclen == 0 at seek pos " + seek + " in file " + heapFile);
this.file.setLength(seek); // delete everything else at the remaining of the file :-(
break loop;
}
// read key
file.readFully(key, 0, key.length);
} catch (final IOException e) {
// EOF reached
break loop; // terminate loop
}
// check if this record is empty
if (key == null || key[0] == 0) {
// it is an empty record, store to free list
if (reclen > 0) free.put(seek, reclen);
} else {
if (this.ordering.wellformed(key)) {
indexready.consume(key, seek);
key = new byte[keylength];
} else {
// free the lost space
free.put(seek, reclen);
file.seek(seek + 4);
Arrays.fill(key, (byte) 0);
file.write(key); // mark the place as empty record
Log.logWarning("HeapReader", "BLOB " + heapFile.getName() + ": skiped not wellformed key " + UTF8.String(key) + " at seek pos " + seek);
}
}
// new seek position
seek += 4L + reclen;
}
indexready.finish();
// finish the index generation
try {
this.index = indexready.result();
} catch (InterruptedException e) {
Log.logException(e);
} catch (ExecutionException e) {
Log.logException(e);
}
Log.logInfo("HeapReader", "finished index generation for " + heapFile.toString() + ", " + index.size() + " entries, " + free.size() + " gaps.");
}
private void mergeFreeEntries() throws IOException {
// try to merge free entries
if (free.size() > 1) {
int merged = 0;
Map.Entry<Long, Integer> lastFree, nextFree;
final Iterator<Map.Entry<Long, Integer>> i = this.free.entrySet().iterator();
lastFree = i.next();
while (i.hasNext()) {
nextFree = i.next();
//System.out.println("*** DEBUG BLOB: free-seek = " + nextFree.seek + ", size = " + nextFree.size);
// check if they follow directly
if (lastFree.getKey() + lastFree.getValue() + 4 == nextFree.getKey()) {
// merge those records
this.file.seek(lastFree.getKey());
lastFree.setValue(lastFree.getValue() + nextFree.getValue() + 4); // this updates also the free map
this.file.writeInt(lastFree.getValue());
this.file.seek(nextFree.getKey());
this.file.writeInt(0);
i.remove();
merged++;
} else {
lastFree = nextFree;
}
}
Log.logInfo("HeapReader", "BLOB " + heapFile.toString() + ": merged " + merged + " free records");
if (merged > 0) deleteFingerprint();
}
}
public String name() {
return this.heapFile.toString();
}
public File location() {
return this.heapFile;
}
/**
* the number of BLOBs in the heap
* @return the number of BLOBs in the heap
*/
public int size() {
if (this.index == null) return 0;
synchronized (index) {
return (this.index == null) ? 0 : this.index.size();
}
}
public boolean isEmpty() {
if (this.index == null) return true;
synchronized (index) {
return this.index.isEmpty();
}
}
/**
* test if a key is in the heap file. This does not need any IO, because it uses only the ram index
* @param key
* @return true if the key exists, false otherwise
*/
public boolean containsKey(byte[] key) {
assert index != null;
key = normalizeKey(key);
synchronized (this.index) {
// check if the file index contains the key
return index.get(key) >= 0;
}
}
public ByteOrder ordering() {
return this.ordering;
}
/**
* find a special key in the heap: the one with the smallest key
* this method is useful if the entries are ordered using their keys.
* then the key with the smallest key denotes the first entry
* @return the smallest key in the heap
* @throws IOException
*/
protected synchronized byte[] firstKey() throws IOException {
synchronized (this.index) {
return index.smallestKey();
}
}
/**
* find a special blob in the heap: one that has the smallest key
* this method is useful if the entries are ordered using their keys.
* then the key with the smallest key denotes the first entry
* @return the entry which key is the smallest in the heap
* @throws IOException
*/
protected byte[] first() throws IOException, RowSpaceExceededException {
synchronized (this.index) {
byte[] key = index.smallestKey();
if (key == null) return null;
return get(key);
}
}
/**
* find a special key in the heap: the one with the largest key
* this method is useful if the entries are ordered using their keys.
* then the key with the largest key denotes the last entry
* @return the largest key in the heap
* @throws IOException
*/
protected byte[] lastKey() throws IOException {
synchronized (this.index) {
return index.largestKey();
}
}
/**
* find a special blob in the heap: one that has the largest key
* this method is useful if the entries are ordered using their keys.
* then the key with the largest key denotes the last entry
* @return the entry which key is the smallest in the heap
* @throws IOException
*/
protected byte[] last() throws IOException, RowSpaceExceededException {
synchronized (this.index) {
byte[] key = index.largestKey();
if (key == null) return null;
return get(key);
}
}
/**
* read a blob from the heap
* @param key
* @return
* @throws IOException
*/
public byte[] get(byte[] key) throws IOException, RowSpaceExceededException {
if (this.index == null) return null;
key = normalizeKey(key);
synchronized (this.index) {
// check if the index contains the key
final long pos = index.get(key);
if (pos < 0) return null;
// access the file and read the container
file.seek(pos);
final int len = file.readInt() - index.row().primaryKeyLength;
if (len < 0) {
// database file may be corrupted and should be deleted :-((
Log.logSevere("HeapReader", "file " + file.file() + " corrupted at " + pos + ": negative len. len = " + len + ", pk.len = " + index.row().primaryKeyLength);
// to get lazy over that problem (who wants to tell the user to stop operation and delete the file???) we work on like the entry does not exist
index.remove(key);
return null;
}
long memr = len + index.row().primaryKeyLength + 64;
if (MemoryControl.available() < memr) {
if (!MemoryControl.request(memr, true)) throw new RowSpaceExceededException(memr, "HeapReader.get()/check"); // not enough memory available for this blob
}
// read the key
byte[] keyf;
try {
keyf = new byte[index.row().primaryKeyLength];
} catch (OutOfMemoryError e) {
throw new RowSpaceExceededException(index.row().primaryKeyLength, "HeapReader.get()/keyf");
}
file.readFully(keyf, 0, keyf.length);
if (!this.ordering.equal(key, keyf)) {
// verification of the indexed access failed. we must re-read the index
Log.logSevere("HeapReader", "indexed verification access failed for " + heapFile.toString());
// this is a severe operation, it should never happen.
// remove entry from index because keeping that element in the index would not make sense
index.remove(key);
// nothing to return
return null;
// but if the process ends in this state, it would completely fail
// if the index is not rebuild now at once
//initIndexReadFromHeap();
}
// read the blob
byte[] blob;
try {
blob = new byte[len];
} catch (OutOfMemoryError e) {
throw new RowSpaceExceededException(len, "HeapReader.get()/blob");
}
file.readFully(blob, 0, blob.length);
return blob;
}
}
public byte[] get(Object key) {
if (!(key instanceof byte[])) return null;
try {
return get((byte[]) key);
} catch (IOException e) {
Log.logException(e);
} catch (RowSpaceExceededException e) {
Log.logException(e);
}
return null;
}
protected boolean checkKey(byte[] key, final long pos) throws IOException {
key = normalizeKey(key);
file.seek(pos);
file.readInt(); // skip the size value
// read the key
final byte[] keyf = new byte[index.row().primaryKeyLength];
file.readFully(keyf, 0, keyf.length);
return this.ordering.equal(key, keyf);
}
/**
* retrieve the size of the BLOB. This should not be used excessively, because it depends on IO operations.
* @param key
* @return the size of the BLOB or -1 if the BLOB does not exist
* @throws IOException
*/
public long length(byte[] key) throws IOException {
key = normalizeKey(key);
synchronized (this.index) {
// check if the index contains the key
final long pos = index.get(key);
if (pos < 0) return -1;
// access the file and read the size of the container
file.seek(pos);
return file.readInt() - index.row().primaryKeyLength;
}
}
/**
* close the BLOB table
*/
public void close(boolean writeIDX) {
synchronized (this.index) {
if (file != null)
try {
file.close();
} catch (IOException e) {
Log.logException(e);
}
file = null;
if (writeIDX && index != null && free != null && (index.size() > 3 || free.size() > 3)) {
// now we can create a dump of the index and the gap information
// to speed up the next start
try {
String fingerprint = fingerprintFileHash(this.heapFile);
if (fingerprint == null) {
Log.logSevere("HeapReader", "cannot write a dump for " + heapFile.getName()+ ": fingerprint is null");
} else {
File newFingerprintFileGap = HeapWriter.fingerprintGapFile(this.heapFile, fingerprint);
if (this.fingerprintFileGap != null &&
this.fingerprintFileGap.getName().equals(newFingerprintFileGap.getName()) &&
this.fingerprintFileGap.exists()) {
Log.logInfo("HeapReader", "using existing gap dump instead of writing a new one: " + this.fingerprintFileGap.getName());
} else {
long start = System.currentTimeMillis();
free.dump(newFingerprintFileGap);
Log.logInfo("HeapReader", "wrote a dump for the " + this.free.size() + " gap entries of " + heapFile.getName()+ " in " + (System.currentTimeMillis() - start) + " milliseconds.");
}
}
free.clear();
free = null;
if (fingerprint != null) {
File newFingerprintFileIdx = HeapWriter.fingerprintIndexFile(this.heapFile, fingerprint);
if (this.fingerprintFileIdx != null &&
this.fingerprintFileIdx.getName().equals(newFingerprintFileIdx.getName()) &&
this.fingerprintFileIdx.exists()) {
Log.logInfo("HeapReader", "using existing idx dump instead of writing a new one: " + this.fingerprintFileIdx.getName());
} else {
long start = System.currentTimeMillis();
index.dump(newFingerprintFileIdx);
Log.logInfo("HeapReader", "wrote a dump for the " + this.index.size() + " index entries of " + heapFile.getName()+ " in " + (System.currentTimeMillis() - start) + " milliseconds.");
}
}
index.close();
index = null;
} catch (IOException e) {
Log.logException(e);
}
}
if (free != null) free.clear();
free = null;
if (index != null) index.close();
index = null;
}
}
public synchronized void close() {
close(true);
}
@Override
public void finalize() {
this.close();
}
/**
* ask for the length of the primary key
* @return the length of the key
*/
public int keylength() {
return this.index.row().primaryKeyLength;
}
/**
* iterator over all keys
* @param up
* @param rotating
* @return
* @throws IOException
*/
public CloneableIterator<byte[]> keys(final boolean up, final boolean rotating) throws IOException {
synchronized (this.index) {
return new RotateIterator<byte[]>(this.index.keys(up, null), null, this.index.size());
}
}
/**
* iterate over all keys
* @param up
* @param firstKey
* @return
* @throws IOException
*/
public CloneableIterator<byte[]> keys(final boolean up, final byte[] firstKey) throws IOException {
synchronized (this.index) {
return this.index.keys(up, firstKey);
}
}
public long length() {
synchronized (this.index) {
return this.heapFile.length();
}
}
/**
* static iterator of entries in BLOBHeap files:
* this is used to import heap dumps into a write-enabled index heap
*/
public static class entries extends LookAheadIterator<Map.Entry<byte[], byte[]>> implements
CloneableIterator<Map.Entry<byte[], byte[]>>,
Iterator<Map.Entry<byte[], byte[]>>,
Iterable<Map.Entry<byte[], byte[]>> {
DataInputStream is;
int keylen;
private final File blobFile;
public entries(final File blobFile, final int keylen) throws IOException {
if (!(blobFile.exists())) throw new IOException("file " + blobFile + " does not exist");
try {
this.is = new DataInputStream(new BufferedInputStream(new FileInputStream(blobFile), 8*1024*1024));
} catch (OutOfMemoryError e) {
this.is = new DataInputStream(new FileInputStream(blobFile));
}
this.keylen = keylen;
this.blobFile = blobFile;
}
public CloneableIterator<Entry<byte[], byte[]>> clone(Object modifier) {
// if the entries iterator is cloned, close the file!
if (is != null) try { is.close(); } catch (final IOException e) {}
is = null;
try {
return new entries(blobFile, keylen);
} catch (IOException e) {
Log.logException(e);
return null;
}
}
public Map.Entry<byte[], byte[]> next0() {
try {
byte b;
int len;
byte[] payload;
byte[] key;
final int keylen1 = this.keylen - 1;
while (true) {
len = is.readInt();
if (len == 0) continue; // rare, but possible: zero length record (takes 4 bytes)
b = is.readByte(); // read a single by te to check for empty record
if (b == 0) {
// this is empty
// read some more bytes to consume the empty record
if (len > 1) {
if (len - 1 != is.skipBytes(len - 1)) { // all that is remaining
Log.logWarning("HeapReader", "problem skiping " + + len + " bytes in " + this.blobFile.getName());
return null;
}
}
continue;
}
// we are now ahead of remaining this.keylen - 1 bytes of the key
key = new byte[this.keylen];
key[0] = b; // the first entry that we know already
if (is.read(key, 1, keylen1) < keylen1) return null; // read remaining key bytes
// so far we have read this.keylen - 1 + 1 = this.keylen bytes.
// there must be a remaining number of len - this.keylen bytes left for the BLOB
if (len < this.keylen) return null; // a strange case that can only happen in case of corrupted data
try {
payload = new byte[len - this.keylen]; // the remaining record entries
if (is.read(payload) < payload.length) return null;
return new entry(key, payload);
} catch (OutOfMemoryError e) {
// the allocation of memory for the payload may fail
// this is bad because we must interrupt the iteration here but the
// process that uses the iteration may think that the iteraton has just been completed
Log.logSevere("HeapReader", "out of memory in LookAheadIterator.next0", e);
return null;
}
}
} catch (final IOException e) {
return null;
}
}
public void close() {
if (is != null) try { is.close(); } catch (final IOException e) {}
is = null;
}
@Override
protected void finalize() {
this.close();
}
}
public static class entry implements Map.Entry<byte[], byte[]> {
private final byte[] s;
private byte[] b;
public entry(final byte[] s, final byte[] b) {
this.s = s;
this.b = b;
}
public byte[] getKey() {
return s;
}
public byte[] getValue() {
return b;
}
public byte[] setValue(byte[] value) {
byte[] b1 = b;
b = value;
return b1;
}
}
public static void main(final String args[]) {
File f = new File(args[0]);
try {
entries hr = new HeapReader.entries(f, 12);
Map.Entry<byte[], byte[]> entry;
while (hr.hasNext()) {
entry = hr.next();
System.out.println(ASCII.String(entry.getKey()) + ":" + UTF8.String(entry.getValue()));
}
} catch (IOException e) {
Log.logException(e);
}
}
}