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yacy_search_server/source/net/yacy/kelondro/table/Table.java

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// Table.java
// (C) 2008 by Michael Peter Christen; mc@yacy.net, Frankfurt a. M., Germany
// first published 14.01.2008 on http://yacy.net
//
// $LastChangedDate$
// $LastChangedRevision$
// $LastChangedBy$
//
// 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.table;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.ConcurrentModificationException;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import java.util.TreeSet;
import net.yacy.cora.document.encoding.ASCII;
import net.yacy.cora.order.CloneableIterator;
import net.yacy.cora.order.NaturalOrder;
import net.yacy.cora.storage.HandleMap;
import net.yacy.cora.util.ConcurrentLog;
import net.yacy.cora.util.SpaceExceededException;
import net.yacy.kelondro.index.Column;
import net.yacy.kelondro.index.Index;
import net.yacy.kelondro.index.Row;
import net.yacy.kelondro.index.Row.Entry;
import net.yacy.kelondro.index.RowCollection;
import net.yacy.kelondro.index.RowHandleMap;
import net.yacy.kelondro.index.RowSet;
import net.yacy.kelondro.io.BufferedRecords;
import net.yacy.kelondro.io.Records;
import net.yacy.kelondro.util.FileUtils;
import net.yacy.kelondro.util.MemoryControl;
import net.yacy.kelondro.util.kelondroException;
/*
* The Table builds upon the EcoFS and tries to reduce the number of IO requests that the
* EcoFS must do to a minimum. In best cases, no IO has to be done for read operations (complete database shadow in RAM)
* and a rare number of write IO operations must be done for a large number of table-writings (using the write buffer of EcoFS)
* To make the Table scalable in question of available RAM, there are two elements that must be scalable:
* - the access index can be either completely in RAM (kelondroRAMIndex) or it is file-based (kelondroTree)
* - the content cache can be either a complete RAM-based shadow of the File, or empty.
* The content cache can also be deleted during run-time, if the available RAM gets too low.
*/
public class Table implements Index, Iterable<Row.Entry> {
// static tracker objects
private final static ConcurrentLog log = new ConcurrentLog("TABLE");
private final static TreeMap<String, Table> tableTracker = new TreeMap<String, Table>();
private final static long maxarraylength = 134217727L; // (2^27-1) that may be the maximum size of array length in some JVMs
private final long minmemremaining; // if less than this memory is remaininig, the memory copy of a table is abandoned
private final int buffersize;
private final Row rowdef;
private final Row taildef;
private HandleMap index;
private BufferedRecords file;
private RowSet table;
public Table(
final File tablefile,
final Row rowdef,
final int buffersize,
final int initialSpace,
boolean useTailCache,
final boolean exceed134217727,
final boolean warmUp) throws SpaceExceededException, kelondroException {
this.rowdef = rowdef;
this.buffersize = buffersize;
this.minmemremaining = Math.max(200L * 1024L * 1024L, MemoryControl.available() / 10);
//this.fail = 0;
// define the taildef, a row like the rowdef but without the first column
final Column[] cols = new Column[rowdef.columns() - 1];
for (int i = 0; i < cols.length; i++) {
cols[i] = rowdef.column(i + 1);
}
this.taildef = new Row(cols, NaturalOrder.naturalOrder);
// initialize table file
boolean freshFile = false;
if (!tablefile.exists()) {
// make new file
freshFile = true;
FileOutputStream fos = null;
tablefile.getParentFile().mkdirs();
try {
fos = new FileOutputStream(tablefile);
} catch (final FileNotFoundException e) {
// should not happen
log.severe("", e);
} finally {
if (fos != null) try { fos.close(); } catch (final IOException e) {}
}
}
try {
// open an existing table file
final int fileSize = (int) tableSize(tablefile, rowdef.objectsize, true);
// initialize index and copy table
final int records = Math.max(fileSize, initialSpace);
final long neededRAM4table = 200L * 1024L * 1024L + records * (this.taildef.objectsize + rowdef.primaryKeyLength + 4L) * 3L / 2L;
this.table = null;
try {
this.table = ((exceed134217727 || neededRAM4table < maxarraylength) &&
useTailCache && MemoryControl.available() > 600L * 1024L * 1024L &&
MemoryControl.request(neededRAM4table, true)) ? new RowSet(this.taildef, records) : null;
} catch (final SpaceExceededException e) {
this.table = null;
} catch (final Throwable e) {
this.table = null;
}
if (log.isFine()) log.fine("initialization of " + tablefile.getName() + ". table copy: " + ((this.table == null) ? "no" : "yes") + ", available RAM: " + (MemoryControl.available() / 1024L / 1024L) + "MB, needed: " + (neededRAM4table / 1024L / 1024L) + "MB, allocating space for " + records + " entries");
final long neededRAM4index = 100L * 1024L * 1024L + records * (rowdef.primaryKeyLength + 4L) * 3L / 2L;
if (records > 0 && !MemoryControl.request(neededRAM4index, true)) {
// despite calculations seemed to show that there is enough memory for the table AND the index
// there is now not enough memory left for the index. So delete the table again to free the memory
// for the index
log.severe(tablefile.getName() + ": not enough RAM (" + (MemoryControl.available() / 1024L / 1024L) + "MB) left for index, deleting allocated table space to enable index space allocation (needed: " + (neededRAM4index / 1024L / 1024L) + "MB)");
this.table = null; System.gc();
log.severe(tablefile.getName() + ": RAM after releasing the table: " + (MemoryControl.available() / 1024L / 1024L) + "MB");
}
this.index = new RowHandleMap(rowdef.primaryKeyLength, rowdef.objectOrder, 4, records, tablefile.getAbsolutePath());
final RowHandleMap errors = new RowHandleMap(rowdef.primaryKeyLength, NaturalOrder.naturalOrder, 4, records, tablefile.getAbsolutePath() + ".errors");
if (log.isFine()) log.fine(tablefile + ": TABLE " + tablefile.toString() + " has table copy " + ((this.table == null) ? "DISABLED" : "ENABLED"));
// read all elements from the file into the copy table
if (log.isFine()) log.fine("initializing RAM index for TABLE " + tablefile.getName() + ", please wait.");
int i = 0;
byte[] key;
if (this.table == null) {
final Iterator<byte[]> ki = new ChunkIterator(tablefile, rowdef.objectsize, rowdef.primaryKeyLength);
while (ki.hasNext()) {
key = ki.next();
// write the key into the index table
assert key != null;
if (key == null) {i++; continue;}
if (rowdef.objectOrder.wellformed(key)) {
this.index.putUnique(key, i++);
} else {
errors.putUnique(key, i++);
}
}
} else {
byte[] record;
key = new byte[rowdef.primaryKeyLength];
final ChunkIterator ri = new ChunkIterator(tablefile, rowdef.objectsize, rowdef.objectsize);
while (ri.hasNext()) {
record = ri.next();
assert record != null;
if (record == null) {i++; continue;}
System.arraycopy(record, 0, key, 0, rowdef.primaryKeyLength);
// write the key into the index table
if (rowdef.objectOrder.wellformed(key)) {
this.index.putUnique(key, i++);
// write the tail into the table
try {
this.table.addUnique(this.taildef.newEntry(record, rowdef.primaryKeyLength, true));
} catch (final SpaceExceededException e) {
this.table = null;
ri.close(); // close inputstream of chunkiterator
break;
}
} else {
errors.putUnique(key, i++);
}
}
Runtime.getRuntime().gc();
if (abandonTable()) {
this.table = null;
}
}
optimize();
// open the file
this.file = new BufferedRecords(new Records(tablefile, rowdef.objectsize), this.buffersize);
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size() + ", file = " + filename();
// clean up the file by cleaning badly formed entries
final int errorc = errors.size();
int errorcc = 0;
int idx;
for (final Map.Entry<byte[], Long> entry: errors) {
idx = (int) entry.getValue().longValue();
removeInFile(idx);
key = entry.getKey();
if (key == null) continue;
log.warn("removing not well-formed entry " + idx + " with key: " + NaturalOrder.arrayList(key, 0, key.length) + ", " + errorcc++ + "/" + errorc);
}
errors.close();
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size() + ", file = " + filename();
// warm up
if (!freshFile && warmUp) {warmUp0();}
} catch (final FileNotFoundException e) {
// should never happen
log.severe("", e);
throw new kelondroException(e.getMessage());
} catch (final IOException e) {
log.severe("", e);
throw new kelondroException(e.getMessage());
}
// track this table
synchronized (tableTracker) {tableTracker.put(tablefile.toString(), this);}
}
public synchronized void warmUp() {
warmUp0();
}
private void warmUp0() {
// remove doubles
try {
final ArrayList<long[]> doubles = this.index.removeDoubles();
//assert index.size() + doubles.size() == i;
//System.out.println(" -removed " + doubles.size() + " doubles- done.");
if (doubles.isEmpty()) return;
log.info(filename() + ": WARNING - TABLE " + filename() + " has " + doubles.size() + " doubles");
// from all the doubles take one, put it back to the index and remove the others from the file
// first put back one element each
final byte[] record = new byte[this.rowdef.objectsize];
final byte[] key = new byte[this.rowdef.primaryKeyLength];
for (final long[] ds: doubles) {
this.file.get((int) ds[0], record, 0);
System.arraycopy(record, 0, key, 0, this.rowdef.primaryKeyLength);
this.index.putUnique(key, (int) ds[0]);
}
// then remove the other doubles by removing them from the table, but do a re-indexing while doing that
// first aggregate all the delete positions because the elements from the top positions must be removed first
final TreeSet<Long> delpos = new TreeSet<Long>();
for (final long[] ds: doubles) {
for (int j = 1; j < ds.length; j++) delpos.add(ds[j]);
}
// now remove the entries in a sorted way (top-down)
Long top;
while (!delpos.isEmpty()) {
top = delpos.last();
delpos.remove(top);
removeInFile(top.intValue());
}
} catch (final SpaceExceededException e) {
log.severe("", e);
} catch (final IOException e) {
log.severe("", e);
}
optimize();
}
@Override
public void optimize() {
this.index.optimize();
if (this.table != null) this.table.optimize();
}
@Override
public long mem() {
return this.index.mem() + ((this.table == null) ? 0 : this.table.mem());
}
private boolean abandonTable() {
// check if not enough memory is there to maintain a memory copy of the table
return MemoryControl.shortStatus() || MemoryControl.available() < this.minmemremaining;
}
@Override
public byte[] smallestKey() {
return this.index.smallestKey();
}
@Override
public byte[] largestKey() {
return this.index.largestKey();
}
public static long tableSize(final File tablefile, final int recordsize, final boolean fixIfCorrupted) throws kelondroException {
try {
return Records.tableSize(tablefile, recordsize);
} catch (final IOException e) {
if (!fixIfCorrupted) {
log.severe("table size broken for file " + tablefile.toString(), e);
throw new kelondroException(e.getMessage());
}
log.severe("table size broken, try to fix " + tablefile.toString());
try {
Records.fixTableSize(tablefile, recordsize);
log.info("successfully fixed table file " + tablefile.toString());
return Records.tableSize(tablefile, recordsize);
} catch (final IOException ee) {
log.severe("table size fix did not work", ee);
throw new kelondroException(e.getMessage());
}
}
}
public static final Iterator<String> filenames() {
// iterates string objects; all file names from record tracker
return tableTracker.keySet().iterator();
}
public static final Map<StatKeys, String> memoryStats(final String filename) {
// returns a map for each file in the tracker;
// the map represents properties for each record objects,
// i.e. for cache memory allocation
final Table theTABLE = tableTracker.get(filename);
return theTABLE.memoryStats();
}
public enum StatKeys {
tableSize, tableKeyChunkSize, tableKeyMem, tableValueChunkSize, tableValueMem
}
private final Map<StatKeys, String> memoryStats() {
// returns statistical data about this object
synchronized (this) {
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
}
final HashMap<StatKeys, String> map = new HashMap<StatKeys, String>(8);
if (this.index == null) return map; // possibly closed or beeing closed
map.put(StatKeys.tableSize, Integer.toString(this.index.size()));
map.put(StatKeys.tableKeyChunkSize, (this.index instanceof RowHandleMap) ? Integer.toString(((RowHandleMap) this.index).row().objectsize) : "-1");
map.put(StatKeys.tableKeyMem, (this.index instanceof RowHandleMap) ? Integer.toString(((RowHandleMap) this.index).row().objectsize * this.index.size()) : "-1");
map.put(StatKeys.tableValueChunkSize, (this.table == null) ? "0" : Integer.toString(this.table.row().objectsize));
map.put(StatKeys.tableValueMem, (this.table == null) ? "0" : Integer.toString(this.table.row().objectsize * this.table.size()));
return map;
}
public boolean usesFullCopy() {
return this.table != null;
}
public static long staticRAMIndexNeed(final File f, final Row rowdef) {
return (((rowdef.primaryKeyLength + 4)) * tableSize(f, rowdef.objectsize, true) * RowCollection.growfactorLarge100 / 100L);
}
public boolean consistencyCheck() {
try {
return this.file.size() == this.index.size();
} catch (final IOException e) {
ConcurrentLog.logException(e);
return false;
}
}
@Override
public synchronized void addUnique(final Entry row) throws IOException, SpaceExceededException {
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
final int i = (int) this.file.size();
try {
this.index.putUnique(row.getPrimaryKeyBytes(), i);
} catch (final SpaceExceededException e) {
if (this.table == null) throw e; // in case the table is not used, there is no help here
this.table = null;
// try again with less memory
this.index.putUnique(row.getPrimaryKeyBytes(), i);
}
final byte[] rowbytes = row.bytes();
if (this.table != null) {
assert this.table.size() == i;
try {
this.table.addUnique(this.taildef.newEntry(rowbytes, this.rowdef.primaryKeyLength, true));
} catch (final SpaceExceededException e) {
this.table = null;
}
if (abandonTable()) this.table = null;
}
this.file.add(rowbytes, 0);
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
}
public synchronized void addUnique(final List<Entry> rows) throws IOException, SpaceExceededException {
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
for (final Entry entry: rows) {
try {
addUnique(entry);
} catch (final SpaceExceededException e) {
if (this.table == null) throw e;
this.table = null;
addUnique(entry);
}
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
}
/**
* @throws SpaceExceededException
* remove double-entries from the table
* this process calls the underlying removeDoubles() method from the table index
* and
* @throws
*/
@Override
public synchronized List<RowCollection> removeDoubles() throws IOException, SpaceExceededException {
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
final List<RowCollection> report = new ArrayList<RowCollection>();
RowSet rows;
final TreeSet<Long> d = new TreeSet<Long>();
final byte[] b = new byte[this.rowdef.objectsize];
Row.Entry inconsistentEntry;
// iterate over all entries that have inconsistent index references
long lastlog = System.currentTimeMillis();
List<long[]> doubles;
try {
doubles = this.index.removeDoubles();
} catch (final SpaceExceededException e) {
if (this.table == null) throw e;
this.table = null;
doubles = this.index.removeDoubles();
}
for (final long[] is: doubles) {
// 'is' is the set of all indexes, that have the same reference
// we collect that entries now here
rows = new RowSet(this.rowdef, is.length);
for (final long L : is) {
assert (int) L < this.file.size() : "L.intValue() = " + (int) L + ", file.size = " + this.file.size(); // prevent ooBounds Exception
d.add(L);
if ((int) L >= this.file.size()) continue; // prevent IndexOutOfBoundsException
this.file.get((int) L, b, 0); // TODO: fix IndexOutOfBoundsException here
inconsistentEntry = this.rowdef.newEntry(b);
try {
rows.addUnique(inconsistentEntry);
} catch (final SpaceExceededException e) {
if (this.table == null) throw e;
this.table = null;
rows.addUnique(inconsistentEntry);
}
}
report.add(rows);
}
// finally delete the affected rows, but start with largest id first, otherwise we overwrite wrong entries
Long s;
while (!d.isEmpty()) {
s = d.last();
d.remove(s);
removeInFile(s.intValue());
if (System.currentTimeMillis() - lastlog > 30000) {
log.info("removing " + d.size() + " entries in " + filename());
lastlog = System.currentTimeMillis();
}
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
return report;
}
@Override
public void close() {
String tablefile = null;
if (this.file != null) {
tablefile = this.file.filename().toString();
this.file.close();
}
this.file = null;
if (this.table != null) this.table.close();
this.table = null;
if (this.index != null) this.index.close();
this.index = null;
if (tablefile != null) tableTracker.remove(tablefile);
}
@Override
protected void finalize() {
if (this.file != null) close();
}
@Override
public String filename() {
return this.file.filename().toString();
}
@Override
public Entry get(final byte[] key, final boolean _forcecopy) throws IOException {
if (this.file == null || this.index == null) return null;
Entry e = get0(key);
if (e != null && this.rowdef.objectOrder.equal(key, e.getPrimaryKeyBytes())) return e;
synchronized (this) {
//assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size() + ", file = " + filename();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size() + ", file = " + filename();
e = get0(key);
assert e == null || this.rowdef.objectOrder.equal(key, e.getPrimaryKeyBytes()) : "key = " + ASCII.String(key) + ", e.k = " + ASCII.String(e.getPrimaryKeyBytes());
return e;
}
}
private Entry get0(final byte[] key) throws IOException {
if (this.file == null || this.index == null) return null;
final int i = (int) this.index.get(key);
if (i == -1) return null;
final byte[] b = new byte[this.rowdef.objectsize];
final Row.Entry cacherow;
if (this.table == null || (cacherow = this.table.get(i, false)) == null) {
// read row from the file
try {
this.file.get(i, b, 0);
} catch (final IndexOutOfBoundsException e) {
// there must be a problem with the table index
log.severe("IndexOutOfBoundsException: " + e.getMessage(), e);
this.index.remove(key);
if (this.table != null) this.table.remove(key);
return null;
}
} else {
// construct the row using the copy in RAM
assert key.length == this.rowdef.primaryKeyLength;
System.arraycopy(key, 0, b, 0, key.length);
System.arraycopy(cacherow.bytes(), 0, b, this.rowdef.primaryKeyLength, this.rowdef.objectsize - this.rowdef.primaryKeyLength);
}
return this.rowdef.newEntry(b);
}
@Override
public Map<byte[], Row.Entry> get(final Collection<byte[]> keys, final boolean forcecopy) throws IOException, InterruptedException {
final Map<byte[], Row.Entry> map = new TreeMap<byte[], Row.Entry>(row().objectOrder);
Row.Entry entry;
for (final byte[] key: keys) {
entry = get(key, forcecopy);
if (entry != null) map.put(key, entry);
}
return map;
}
@Override
public boolean has(final byte[] key) {
if (this.index == null) return false;
return this.index.has(key);
}
@Override
public synchronized CloneableIterator<byte[]> keys(final boolean up, final byte[] firstKey) throws IOException {
return this.index.keys(up, firstKey);
}
@Override
public Entry replace(final Entry row) throws IOException, SpaceExceededException {
assert row != null;
if (this.file == null || row == null) return null;
final byte[] rowb = row.bytes();
assert rowb != null;
if (rowb == null) return null;
final byte[] key = row.getPrimaryKeyBytes();
synchronized (this) {
//assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
//assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
final int i = (int) this.index.get(key);
if (i == -1) {
try {
addUnique(row);
} catch (final SpaceExceededException e) {
if (this.table == null) throw e;
this.table = null;
addUnique(row);
}
return null;
}
final byte[] b = new byte[this.rowdef.objectsize];
Row.Entry cacherow;
if (this.table == null || (cacherow = this.table.get(i, false)) == null) {
// read old value
this.file.get(i, b, 0);
// write new value
this.file.put(i, rowb, 0);
} else {
// read old value
assert cacherow != null;
System.arraycopy(key, 0, b, 0, this.rowdef.primaryKeyLength);
System.arraycopy(cacherow.bytes(), 0, b, this.rowdef.primaryKeyLength, this.rowdef.objectsize - this.rowdef.primaryKeyLength);
// write new value
try {
this.table.set(i, this.taildef.newEntry(rowb, this.rowdef.primaryKeyLength, true));
} catch (final SpaceExceededException e) {
this.table = null;
}
if (abandonTable()) this.table = null;
this.file.put(i, rowb, 0);
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
// return old value
return this.rowdef.newEntry(b);
}
}
/**
* Adds the row to the index. The row is identified by the primary key of the row.
* @param row a index row
* @return true if this set did _not_ already contain the given row.
* @throws IOException
* @throws SpaceExceededException
*/
@Override
public boolean put(final Entry row) throws IOException, SpaceExceededException {
assert row != null;
if (this.file == null || row == null) return true;
final byte[] rowb = row.bytes();
assert rowb != null;
if (rowb == null) return true;
final byte[] key = row.getPrimaryKeyBytes();
synchronized (this) {
//assert this.file == null || this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size() + ", file = " + filename();
//assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size() + ", file = " + filename();
final int i = (int) this.index.get(key);
if (i == -1) {
try {
addUnique(row);
} catch (final SpaceExceededException e) {
if (this.table == null) throw e;
this.table = null;
addUnique(row);
}
return true;
}
if (this.table == null) {
// write new value
this.file.put(i, rowb, 0);
} else {
// write new value
this.file.put(i, rowb, 0);
if (abandonTable()) this.table = null; else try {
this.table.set(i, this.taildef.newEntry(rowb, this.rowdef.primaryKeyLength, true));
} catch (final SpaceExceededException e) {
this.table = null;
}
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
return false;
}
}
/**
* remove one entry from the file
* @param i an index position within the file (not a byte position)
* @throws IOException
* @throws SpaceExceededException
*/
private void removeInFile(final int i) throws IOException, SpaceExceededException {
assert i >= 0;
final byte[] p = new byte[this.rowdef.objectsize];
if (this.table == null) {
if (i == this.index.size() - 1) {
this.file.cleanLast();
} else {
while (this.file.size() > 0) {
this.file.cleanLast(p, 0);
if (!(this.rowdef.objectOrder.wellformed(p, 0, this.rowdef.primaryKeyLength))) {
continue;
}
this.file.put(i, p, 0);
final byte[] k = new byte[this.rowdef.primaryKeyLength];
System.arraycopy(p, 0, k, 0, this.rowdef.primaryKeyLength);
this.index.put(k, i);
break;
}
}
} else {
if (i == this.index.size() - 1) {
// special handling if the entry is the last entry in the file
this.table.removeRow(i, false);
this.file.cleanLast();
} else {
// switch values
final Row.Entry te = this.table.removeOne();
try {
this.table.set(i, te);
} catch (final SpaceExceededException e) {
this.table = null;
}
while (this.file.size() > 0) {
this.file.cleanLast(p, 0);
final Row.Entry lr = this.rowdef.newEntry(p);
if (lr == null) {
// in case that p is not well-formed lr may be null
// drop table copy because that becomes too complicated here
this.table.clear();
this.table = null;
continue;
}
this.file.put(i, p, 0);
byte[] pk = lr.getPrimaryKeyBytes();
if (pk == null) {
// Table file might be corrupt
log.warn("Possible corruption found in table " + this.filename() + " detected. i=" + i + ",p=" + p);
continue;
}
this.index.put(pk, i);
break;
}
}
}
}
@Override
public boolean delete(final byte[] key) throws IOException {
return remove(key) != null;
}
@Override
public synchronized Entry remove(final byte[] key) throws IOException {
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
assert key.length == this.rowdef.primaryKeyLength;
final int i = (int) this.index.get(key);
if (i == -1) return null; // nothing to do
// prepare result
final byte[] b = new byte[this.rowdef.objectsize];
final byte[] p = new byte[this.rowdef.objectsize];
final int sb = this.index.size();
int ix;
assert i < this.index.size();
final Row.Entry cacherow;
if (this.table == null || (cacherow = this.table.get(i, false)) == null) {
if (i == this.index.size() - 1) {
// element is at last entry position
ix = (int) this.index.remove(key);
assert this.index.size() < i + 1 : "index.size() = " + this.index.size() + ", i = " + i;
assert ix == i;
this.file.cleanLast(b, 0);
} else {
// remove entry from index
assert i < this.index.size() - 1 : "index.size() = " + this.index.size() + ", i = " + i;
ix = (int) this.index.remove(key);
assert i < this.index.size() : "index.size() = " + this.index.size() + ", i = " + i;
assert ix == i;
// read element that shall be removed
this.file.get(i, b, 0);
// fill the gap with value from last entry in file
this.file.cleanLast(p, 0);
this.file.put(i, p, 0);
final byte[] k = new byte[this.rowdef.primaryKeyLength];
System.arraycopy(p, 0, k, 0, this.rowdef.primaryKeyLength);
try {
this.index.put(k, i);
} catch (final SpaceExceededException e) {
ConcurrentLog.logException(e);
throw new IOException("RowSpaceExceededException: " + e.getMessage());
}
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
} else {
// get result value from the table copy, so we don't need to read it from the file
System.arraycopy(key, 0, b, 0, key.length);
System.arraycopy(cacherow.bytes(), 0, b, this.rowdef.primaryKeyLength, this.taildef.objectsize);
if (i == this.index.size() - 1) {
// special handling if the entry is the last entry in the file
ix = (int) this.index.remove(key);
assert this.index.size() < i + 1 : "index.size() = " + this.index.size() + ", i = " + i;
assert ix == i;
this.table.removeRow(i, false);
this.file.cleanLast();
} else {
// remove entry from index
ix = (int) this.index.remove(key);
assert i < this.index.size() : "index.size() = " + this.index.size() + ", i = " + i;
assert ix == i;
// switch values:
// remove last entry from the file copy to fill it in the gap
final Row.Entry te = this.table.removeOne();
// fill the gap in file copy
try {
this.table.set(i, te);
} catch (final SpaceExceededException e) {
ConcurrentLog.logException(e);
this.table = null;
}
// move entry from last entry in file to gap position
this.file.cleanLast(p, 0);
this.file.put(i, p, 0);
// set new index for moved entry in index
final Row.Entry lr = this.rowdef.newEntry(p);
try {
this.index.put(lr.getPrimaryKeyBytes(), i);
} catch (final SpaceExceededException e) {
this.table = null;
throw new IOException("RowSpaceExceededException: " + e.getMessage());
}
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
}
assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
assert this.index.size() + 1 == sb : "index.size() = " + this.index.size() + ", sb = " + sb;
return this.rowdef.newEntry(b);
}
@Override
public synchronized Entry removeOne() throws IOException {
//assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
final byte[] le = new byte[this.rowdef.objectsize];
final long fsb = this.file.size();
assert fsb != 0 : "file.size() = " + fsb;
this.file.cleanLast(le, 0);
assert this.file.size() < fsb : "file.size() = " + this.file.size();
final Row.Entry lr = this.rowdef.newEntry(le);
assert lr != null;
assert lr.getPrimaryKeyBytes() != null;
final int is = this.index.size();
assert this.index.has(lr.getPrimaryKeyBytes());
final int i = (int) this.index.remove(lr.getPrimaryKeyBytes());
assert i < 0 || this.index.size() < is : "index.size() = " + this.index.size() + ", is = " + is;
assert i >= 0;
if (this.table != null) {
final int tsb = this.table.size();
this.table.removeOne();
assert this.table.size() < tsb : "table.size() = " + this.table.size() + ", tsb = " + tsb;
}
//assert this.file.size() == this.index.size() : "file.size() = " + this.file.size() + ", index.size() = " + this.index.size();
assert this.table == null || this.table.size() == this.index.size() : "table.size() = " + this.table.size() + ", index.size() = " + this.index.size();
return lr;
}
@Override
public List<Row.Entry> top(int count) throws IOException {
if (count > this.size()) count = this.size();
final ArrayList<Row.Entry> list = new ArrayList<Row.Entry>();
if (this.file == null || this.index == null || this.size() == 0 || count == 0) return list;
long i = this.file.size() - 1;
while (count > 0 && i >= 0) {
final byte[] b = new byte[this.rowdef.objectsize];
this.file.get(i, b, 0);
list.add(this.rowdef.newEntry(b));
i--;
count--;
}
return list;
}
@Override
public List<Row.Entry> random(int count) throws IOException {
if (count > this.size()) count = this.size();
final ArrayList<Row.Entry> list = new ArrayList<Row.Entry>();
if (this.file == null || this.index == null || this.size() == 0 || count == 0) return list;
long cursor = 0;
int stepsize = this.size() / count;
while (count > 0 && cursor < this.size()) {
final byte[] b = new byte[this.rowdef.objectsize];
this.file.get(cursor, b, 0);
list.add(this.rowdef.newEntry(b));
count--;
cursor += stepsize;
}
return list;
}
@Override
public synchronized void clear() throws IOException {
this.file.clear();
// initialize index and copy table
this.table = (this.table == null) ? null : new RowSet(this.taildef);
this.index.clear();
}
@Override
public Row row() {
return this.rowdef;
}
@Override
public int size() {
if (this.index == null) return 0;
return this.index.size();
}
@Override
public boolean isEmpty() {
return this.index == null || this.index.isEmpty();
}
@Override
public Iterator<Entry> iterator() {
try {
return rows();
} catch (final IOException e) {
return null;
}
}
@Override
public synchronized CloneableIterator<Entry> rows() throws IOException {
this.file.flushBuffer();
return new rowIteratorNoOrder();
}
private class rowIteratorNoOrder implements CloneableIterator<Entry> {
Iterator<Map.Entry<byte[], Long>> i;
long idx;
byte[] key;
public rowIteratorNoOrder() {
// don't use the ChunkIterator here because it may create too many open files during string load
//ri = new ChunkIterator(tablefile, rowdef.objectsize, rowdef.objectsize);
this.i = Table.this.index.iterator();
}
@Override
public CloneableIterator<Entry> clone(final Object modifier) {
return new rowIteratorNoOrder();
}
@Override
public boolean hasNext() {
return this.i != null && this.i.hasNext();
}
@Override
public Entry next() {
final Map.Entry<byte[], Long> entry = this.i.next();
if (entry == null) return null;
this.key = entry.getKey();
if (this.key == null) return null;
this.idx = entry.getValue().longValue();
try {
return get(this.key, false);
} catch (final IOException e) {
return null;
}
}
@Override
public void remove() {
if (this.key != null) {
try {
removeInFile((int) this.idx);
} catch (final IOException e) {
} catch (final SpaceExceededException e) {
}
this.i.remove();
}
}
@Override
public void close() {
if (this.i instanceof CloneableIterator) {
((CloneableIterator<Map.Entry<byte[], Long>>) this.i).close();
}
}
}
@Override
public synchronized CloneableIterator<Entry> rows(final boolean up, final byte[] firstKey) throws IOException {
return new rowIterator(up, firstKey);
}
private class rowIterator implements CloneableIterator<Entry> {
private final CloneableIterator<byte[]> i;
private final boolean up;
private final byte[] fk;
private int c;
private rowIterator(final boolean up, final byte[] firstKey) {
this.up = up;
this.fk = firstKey;
this.i = Table.this.index.keys(up, firstKey);
this.c = -1;
}
@Override
public CloneableIterator<Entry> clone(final Object modifier) {
return new rowIterator(this.up, this.fk);
}
@Override
public boolean hasNext() {
return this.i.hasNext();
}
@Override
public Entry next() {
final byte[] k = this.i.next();
assert k != null;
if (k == null) return null;
this.c = (int) Table.this.index.get(k);
if (this.c < 0) throw new ConcurrentModificationException(); // this should only happen if the table was modified during the iteration
final byte[] b = new byte[Table.this.rowdef.objectsize];
final Row.Entry cacherow;
if (Table.this.table == null || (cacherow = Table.this.table.get(this.c, false)) == null) {
// read from file
try {
Table.this.file.get(this.c, b, 0);
} catch (final IOException e) {
log.severe("", e);
return null;
}
} else {
// compose from table and key
System.arraycopy(k, 0, b, 0, Table.this.rowdef.primaryKeyLength);
System.arraycopy(cacherow.bytes(), 0, b, Table.this.rowdef.primaryKeyLength, Table.this.taildef.objectsize);
}
return Table.this.rowdef.newEntry(b);
}
@Override
public void remove() {
throw new UnsupportedOperationException("no remove in Table.rowIterator");
}
@Override
public void close() {
this.i.close();
}
}
private static byte[] testWord(final char c) {
return new byte[]{(byte) c, 32, 32, 32};
}
private static String[] permutations(final int letters) {
String p = "";
for (int i = 0; i < letters; i++) p = p + ((char) (('A') + i));
return permutations(p);
}
private static String[] permutations(final String source) {
if (source.isEmpty()) return new String[0];
if (source.length() == 1) return new String[]{source};
final char c = source.charAt(0);
final String[] recres = permutations(source.substring(1));
final String[] result = new String[source.length() * recres.length];
for (int perm = 0; perm < recres.length; perm++) {
result[perm * source.length()] = c + recres[perm];
for (int pos = 1; pos < source.length() - 1; pos++) {
result[perm * source.length() + pos] = recres[perm].substring(0, pos) + c + recres[perm].substring(pos);
}
result[perm * source.length() + source.length() - 1] = recres[perm] + c;
}
return result;
}
private static Table testTable(final File f, final String testentities, final boolean useTailCache, final boolean exceed134217727) throws IOException, SpaceExceededException {
if (f.exists()) FileUtils.deletedelete(f);
final Row rowdef = new Row("byte[] a-4, byte[] b-4", NaturalOrder.naturalOrder);
final Table tt = new Table(f, rowdef, 100, 0, useTailCache, exceed134217727, true);
byte[] b;
final Row.Entry row = rowdef.newEntry();
for (int i = 0; i < testentities.length(); i++) {
b = testWord(testentities.charAt(i));
row.setCol(0, b);
row.setCol(1, b);
tt.put(row);
}
return tt;
}
private static int countElements(final Table t) {
int count = 0;
for (final Row.Entry row: t) {
count++;
if (row == null) System.out.println("ERROR! null element found");
// else System.out.println("counted element: " + new
// String(n.getKey()));
}
return count;
}
public static void bigtest(final int elements, final File testFile, final boolean useTailCache, final boolean exceed134217727) {
System.out.println("starting big test with " + elements + " elements:");
final long start = System.currentTimeMillis();
final String[] s = permutations(elements);
Table tt;
int count;
try {
for (int i = 0; i < s.length; i++) {
System.out.println("*** probing tree " + i + " for permutation " + s[i]);
// generate tree and delete elements
tt = testTable(testFile, s[i], useTailCache, exceed134217727);
count = countElements(tt);
if (count != tt.size()) {
System.out.println("wrong size for " + s[i] + ": count = " + count + ", size() = " + tt.size());
}
tt.close();
for (final String element : s) {
tt = testTable(testFile, s[i], useTailCache, exceed134217727);
// delete by permutation j
for (int elt = 0; elt < element.length(); elt++) {
tt.remove(testWord(element.charAt(elt)));
count = countElements(tt);
if (count != tt.size()) {
System.out.println("ERROR! wrong size for probe tree " + s[i] + "; probe delete " + element + "; position " + elt + "; count = " + count + ", size() = " + tt.size());
}
}
tt.close();
}
}
System.out.println("FINISHED test after " + ((System.currentTimeMillis() - start) / 1000) + " seconds.");
} catch (final Exception e) {
ConcurrentLog.logException(e);
System.out.println("TERMINATED");
}
}
public void print() throws IOException {
System.out.println("PRINTOUT of table, length=" + size());
Entry row;
byte[] key;
final CloneableIterator<byte[]> i = keys(true, null);
while (i.hasNext()) {
System.out.print("row " + i + ": ");
key = i.next();
row = get(key, false);
System.out.println(row.toString());
}
System.out.println("EndOfTable");
}
public static void main(final String[] args) {
// open a file, add one entry and exit
final File f = new File(args[0]);
System.out.println("========= Testcase: no tail cache:");
bigtest(5, f, false, false);
System.out.println("========= Testcase: with tail cache:");
bigtest(5, f, true, true);
/*
kelondroRow row = new kelondroRow("byte[] key-4, byte[] x-5", kelondroNaturalOrder.naturalOrder, 0);
try {
kelondroTABLE t = new kelondroTABLE(f, row);
kelondroRow.Entry entry = row.newEntry();
entry.setCol(0, "abcd".getBytes());
entry.setCol(1, "dummy".getBytes());
t.put(entry);
t.close();
} catch (final IOException e) {
Log.logException(e);
}
*/
}
@Override
public void deleteOnExit() {
this.file.deleteOnExit();
}
}
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