// kelondroEcoIndex.java
// (C) 2008 by Michael Peter Christen; mc@yacy.net, Frankfurt a. M., Germany
// first published 14.01.2008 on http://yacy.net
//
// $LastChangedDate: 2006-04-02 22:40:07 +0200 (So, 02 Apr 2006) $
// $LastChangedRevision: 1986 $
// $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 de.anomic.kelondro;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
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 de.anomic.kelondro.kelondroRow.Entry;
import de.anomic.server.serverMemory;
/*
* The EcoIndex 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 EcoIndex 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 kelondroEcoTable implements kelondroIndex {
// static tracker objects
private static TreeMap<String, kelondroEcoTable> tableTracker = new TreeMap<String, kelondroEcoTable>();
public static final int tailCacheDenyUsage = 0;
public static final int tailCacheForceUsage = 1;
public static final int tailCacheUsageAuto = 2;
public static final long maxarraylength = 134217727L; // that may be the maxmimum size of array length in some JVMs
kelondroRowSet table;
kelondroBytesIntMap index;
kelondroBufferedEcoFS file;
kelondroRow rowdef;
int fail;
kelondroRow taildef;
private int buffersize;
public kelondroEcoTable(File tablefile, kelondroRow rowdef, int useTailCache, int buffersize, int initialSpace) {
this.rowdef = rowdef;
this.buffersize = buffersize;
this.fail = 0;
assert rowdef.primaryKeyIndex == 0;
// define the taildef, a row like the rowdef but without the first column
kelondroColumn[] cols = new kelondroColumn[rowdef.columns() - 1];
for (int i = 0; i < cols.length; i++) {
cols[i] = rowdef.column(i + 1);
}
this.taildef = new kelondroRow(cols, kelondroNaturalOrder.naturalOrder, -1);
// initialize table file
if (!tablefile.exists()) {
// make new file
FileOutputStream fos = null;
try {
fos = new FileOutputStream(tablefile);
} catch (FileNotFoundException e) {
// should not happen
e.printStackTrace();
}
if (fos != null) try { fos.close(); } catch (IOException e) {}
}
try {
// open an existing table file
int fileSize = (int) tableSize(tablefile, rowdef.objectsize);
// initialize index and copy table
int records = (int) Math.max(fileSize, initialSpace);
long neededRAM4table = ((long) records) * (((long) rowdef.objectsize) + 4L) * 3L;
table = ((neededRAM4table < maxarraylength) &&
((useTailCache == tailCacheForceUsage) ||
((useTailCache == tailCacheUsageAuto) && (serverMemory.free() > neededRAM4table + 200 * 1024 * 1024)))) ?
new kelondroRowSet(taildef, records) : null;
System.out.println("*** DEBUG " + tablefile + ": available RAM: " + (serverMemory.available() / 1024 / 1024) + "MB, allocating space for " + records + " entries");
long neededRAM4index = 2 * 1024 * 1024 + records * (rowdef.primaryKeyLength + 4) * 3 / 2;
if (!serverMemory.request(neededRAM4index, false)) {
// 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
System.out.println("*** DEBUG " + tablefile + ": not enough RAM (" + (serverMemory.available() / 1024 / 1024) + "MB) left for index, deleting allocated table space to enable index space allocation (needed: " + (neededRAM4index / 1024 / 1024) + "MB)");
table = null; System.gc();
System.out.println("*** DEBUG " + tablefile + ": RAM after releasing the table: " + (serverMemory.available() / 1024 / 1024) + "MB");
}
index = new kelondroBytesIntMap(rowdef.primaryKeyLength, rowdef.objectOrder, records);
System.out.println("*** DEBUG " + tablefile + ": EcoTable " + tablefile.toString() + " has table copy " + ((table == null) ? "DISABLED" : "ENABLED"));
// read all elements from the file into the copy table
System.out.print("*** initializing RAM index for EcoTable " + tablefile.getName() + ":");
int i = 0;
byte[] key;
if (table == null) {
Iterator<byte[]> ki = keyIterator(tablefile, rowdef);
while (ki.hasNext()) {
key = ki.next();
// write the key into the index table
assert key != null;
if (key == null) {i++; continue;}
if (!index.addi(key, i++)) fail++;
assert index.size() + fail == i : "index.size() = " + index.size() + ", i = " + i + ", fail = " + fail + ", key = '" + new String(key) + "'";
if ((i % 10000) == 0) {
System.out.print('.');
System.out.flush();
}
}
} else {
byte[] record;
key = new byte[rowdef.primaryKeyLength];
Iterator<byte[]> ri = new kelondroEcoFS.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 (!index.addi(key, i++)) fail++;
// write the tail into the table
table.addUnique(taildef.newEntry(record, rowdef.primaryKeyLength, true));
if ((i % 10000) == 0) {
System.out.print('.');
System.out.flush();
}
}
}
// check consistency
System.out.print(" -ordering- ..");
System.out.flush();
this.file = new kelondroBufferedEcoFS(new kelondroEcoFS(tablefile, rowdef.objectsize), this.buffersize);
ArrayList<Integer[]> doubles = index.removeDoubles();
//assert index.size() + doubles.size() + fail == i;
System.out.println(" -removed " + doubles.size() + " doubles- done.");
if (doubles.size() > 0) {
System.out.println("DEBUG " + tablefile + ": WARNING - EcoTable " + tablefile + " 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
byte[] record = new byte[rowdef.objectsize];
key = new byte[rowdef.primaryKeyLength];
for (Integer[] ds: doubles) {
file.get(ds[0].longValue(), record, 0);
System.arraycopy(record, 0, key, 0, rowdef.primaryKeyLength);
if (!index.addi(key, ds[0].intValue())) fail++;
}
// 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
TreeSet<Integer> delpos = new TreeSet<Integer>();
for (Integer[] ds: doubles) {
for (int j = 1; j < ds.length; j++) delpos.add(ds[j]);
}
// now remove the entries in a sorted way (top-down)
Integer top;
while (delpos.size() > 0) {
top = delpos.last();
delpos.remove(top);
removeInFile(top.intValue());
}
}
/* try {
assert file.size() == index.size() + doubles.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size() + ", doubles.size() = " + doubles.size() + ", fail = " + fail + ", i = " + i;
} catch (IOException e) {
e.printStackTrace();
}*/
} catch (FileNotFoundException e) {
// should never happen
e.printStackTrace();
throw new kelondroException(e.getMessage());
} catch (IOException e) {
e.printStackTrace();
throw new kelondroException(e.getMessage());
}
// track this table
tableTracker.put(tablefile.toString(), this);
}
/**
* a KeyIterator
* @param file: the eco-file
* @param rowdef: the row definition
* @throws FileNotFoundException
* @return an iterator for all keys in the file
*/
public Iterator<byte[]> keyIterator(File file, kelondroRow rowdef) throws FileNotFoundException {
assert rowdef.primaryKeyIndex == 0;
return new kelondroEcoFS.ChunkIterator(file, rowdef.objectsize, rowdef.primaryKeyLength);
}
public static long tableSize(File tablefile, int recordsize) {
// returns number of records in table
return kelondroEcoFS.tableSize(tablefile, recordsize);
}
public static final Iterator<String> filenames() {
// iterates string objects; all file names from record tracker
return tableTracker.keySet().iterator();
}
public static final Map<String, String> memoryStats(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
kelondroEcoTable theEcoTable = tableTracker.get(filename);
return theEcoTable.memoryStats();
}
private final Map<String, String> memoryStats() {
// returns statistical data about this object
assert ((table == null) || (table.size() == index.size()));
HashMap<String, String> map = new HashMap<String, String>();
map.put("tableSize", Integer.toString(index.size()));
map.put("tableKeyChunkSize", Integer.toString(index.row().objectsize));
map.put("tableKeyMem", Integer.toString((int) (index.row().objectsize * index.size() * kelondroRowCollection.growfactor)));
map.put("tableValueChunkSize", (table == null) ? "0" : Integer.toString(table.row().objectsize));
map.put("tableValueMem", (table == null) ? "0" : Integer.toString((int) (table.row().objectsize * table.size() * kelondroRowCollection.growfactor)));
return map;
}
public static int staticRAMIndexNeed(File f, kelondroRow rowdef) {
return (int) ((rowdef.primaryKeyLength + 4) * tableSize(f, rowdef.objectsize) * kelondroRowCollection.growfactor);
}
public synchronized boolean addUnique(Entry row) throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
int i = (int) file.size();
boolean added = index.addi(row.getPrimaryKeyBytes(), i);
if (!added) return false;
if (table != null) {
assert table.size() == i;
table.addUnique(taildef.newEntry(row.bytes(), rowdef.primaryKeyLength, true));
}
file.add(row.bytes(), 0);
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
return true;
}
public synchronized int addUniqueMultiple(List<Entry> rows) throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
Iterator<Entry> i = rows.iterator();
int c = 0;
while (i.hasNext()) {
if (addUnique(i.next())) c++;
}
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
return c;
}
public synchronized ArrayList<kelondroRowCollection> removeDoubles() throws IOException {
ArrayList<kelondroRowCollection> report = new ArrayList<kelondroRowCollection>();
kelondroRowSet rows;
TreeSet<Integer> d = new TreeSet<Integer>();
byte[] b = new byte[rowdef.objectsize];
for (Integer[] is: index.removeDoubles()) {
rows = new kelondroRowSet(this.rowdef, is.length);
for (int j = 0; j < is.length; j++) {
d.add(is[j]);
file.get(is[j].intValue(), b, 0); // TODO: fix IndexOutOfBoundsException here
rows.addUnique(rowdef.newEntry(b));
}
report.add(rows);
}
// finally delete the affected rows, but start with largest id first, otherwise we overwrite wrong entries
Integer s;
while (d.size() > 0) {
s = d.last();
d.remove(s);
this.removeInFile(s.intValue());
}
return report;
}
public void close() {
file.close();
file = null;
}
public void finalize() {
if (this.file != null) this.close();
}
public String filename() {
return this.file.filename().toString();
}
public synchronized Entry get(byte[] key) throws IOException {
if ((file == null) || (index == null)) return null;
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size() + ", fail = " + fail;
assert ((table == null) || (table.size() == index.size()));
int i = index.geti(key);
if (i == -1) return null;
byte[] b = new byte[rowdef.objectsize];
if (table == null) {
// read row from the file
file.get(i, b, 0);
} else {
// construct the row using the copy in RAM
kelondroRow.Entry v = table.get(i, false);
assert v != null;
if (v == null) return null;
assert key.length == rowdef.primaryKeyLength;
System.arraycopy(key, 0, b, 0, key.length);
System.arraycopy(v.bytes(), 0, b, rowdef.primaryKeyLength, rowdef.objectsize - rowdef.primaryKeyLength);
}
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
return rowdef.newEntry(b);
}
public synchronized boolean has(byte[] key) throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
return index.geti(key) >= 0;
}
public synchronized kelondroCloneableIterator<byte[]> keys(boolean up, byte[] firstKey) throws IOException {
return index.keys(up, firstKey);
}
public kelondroProfile profile() {
return null;
}
public synchronized Entry put(Entry row) throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
assert row != null;
assert row.bytes() != null;
if ((row == null) || (row.bytes() == null)) return null;
int i = index.geti(row.getPrimaryKeyBytes());
if (i == -1) {
addUnique(row);
return null;
}
byte[] b = new byte[rowdef.objectsize];
if (table == null) {
// read old value
file.get(i, b, 0);
// write new value
file.put(i, row.bytes(), 0);
} else {
// read old value
kelondroRow.Entry v = table.get(i, false);
assert v != null;
System.arraycopy(row.getPrimaryKeyBytes(), 0, b, 0, rowdef.primaryKeyLength);
System.arraycopy(v.bytes(), 0, b, rowdef.primaryKeyLength, rowdef.objectsize - rowdef.primaryKeyLength);
// write new value
table.set(i, taildef.newEntry(row.bytes(), rowdef.primaryKeyLength, true));
file.put(i, row.bytes(), 0);
}
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
// return old value
return rowdef.newEntry(b);
}
public synchronized Entry put(Entry row, Date entryDate) throws IOException {
return put(row);
}
public synchronized void putMultiple(List<Entry> rows) throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
Iterator<Entry> i = rows.iterator();
while (i.hasNext()) {
put(i.next());
}
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
}
private void removeInFile(int i) throws IOException {
assert i >= 0;
byte[] p = new byte[rowdef.objectsize];
if (table == null) {
if (i == index.size() - 1) {
file.cleanLast();
} else {
file.cleanLast(p, 0);
file.put(i, p, 0);
byte[] k = new byte[rowdef.primaryKeyLength];
System.arraycopy(p, 0, k, 0, rowdef.primaryKeyLength);
index.puti(k, i);
}
} else {
if (i == index.size() - 1) {
// special handling if the entry is the last entry in the file
table.removeRow(i, false);
file.cleanLast();
} else {
// switch values
kelondroRow.Entry te = table.removeOne();
table.set(i, te);
file.cleanLast(p, 0);
file.put(i, p, 0);
kelondroRow.Entry lr = rowdef.newEntry(p);
index.puti(lr.getPrimaryKeyBytes(), i);
}
}
}
public synchronized Entry remove(byte[] key, boolean keepOrder) throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
assert keepOrder == false; // this class cannot keep the order during a remove
assert key.length == rowdef.primaryKeyLength;
int i = index.geti(key);
if (i == -1) return null; // nothing to do
// prepare result
byte[] b = new byte[rowdef.objectsize];
byte[] p = new byte[rowdef.objectsize];
int sb = index.size();
int ix;
assert i < index.size();
if (table == null) {
if (i == index.size() - 1) {
ix = index.removei(key);
assert ix == i;
file.cleanLast(b, 0);
} else {
assert i < index.size() - 1;
ix = index.removei(key);
assert ix == i;
file.get(i, b, 0);
file.cleanLast(p, 0);
file.put(i, p, 0);
byte[] k = new byte[rowdef.primaryKeyLength];
System.arraycopy(p, 0, k, 0, rowdef.primaryKeyLength);
index.puti(k, i);
}
assert (file.size() == index.size() + fail);
} else {
// get result value from the table copy, so we don't need to read it from the file
kelondroRow.Entry v = table.get(i, false);
System.arraycopy(key, 0, b, 0, key.length);
System.arraycopy(v.bytes(), 0, b, rowdef.primaryKeyLength, taildef.objectsize);
if (i == index.size() - 1) {
// special handling if the entry is the last entry in the file
ix = index.removei(key);
assert ix == i;
table.removeRow(i, false);
file.cleanLast();
} else {
// switch values
ix = index.removei(key);
assert ix == i;
kelondroRow.Entry te = table.removeOne();
table.set(i, te);
file.cleanLast(p, 0);
file.put(i, p, 0);
kelondroRow.Entry lr = rowdef.newEntry(p);
index.puti(lr.getPrimaryKeyBytes(), i);
}
assert (file.size() == index.size() + fail);
assert (table.size() == index.size()) : "table.size() = " + table.size() + ", index.size() = " + index.size();
}
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
assert index.size() + 1 == sb : "index.size() = " + index.size() + ", sb = " + sb;
return rowdef.newEntry(b);
}
public synchronized Entry removeOne() throws IOException {
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
assert ((table == null) || (table.size() == index.size()));
byte[] le = new byte[rowdef.objectsize];
file.cleanLast(le, 0);
kelondroRow.Entry lr = rowdef.newEntry(le);
int i = index.removei(lr.getPrimaryKeyBytes());
assert i >= 0;
if (table != null) table.removeOne();
assert file.size() == index.size() + fail : "file.size() = " + file.size() + ", index.size() = " + index.size();
return lr;
}
public void clear() throws IOException {
File f = file.filename();
file.close();
f.delete();
// make new file
FileOutputStream fos = null;
try {
fos = new FileOutputStream(f);
} catch (FileNotFoundException e) {
// should not happen
e.printStackTrace();
}
if (fos != null) try { fos.close(); } catch (IOException e) {}
// open an existing table file
try {
this.file = new kelondroBufferedEcoFS(new kelondroEcoFS(f, rowdef.objectsize), this.buffersize);
} catch (FileNotFoundException e) {
// should never happen
e.printStackTrace();
}
// initialize index and copy table
table = new kelondroRowSet(taildef, 1);
index = new kelondroBytesIntMap(rowdef.primaryKeyLength, rowdef.objectOrder, 1);
}
public kelondroRow row() {
return this.rowdef;
}
public synchronized int size() {
return index.size();
}
public synchronized kelondroCloneableIterator<Entry> rows(boolean up, byte[] firstKey) throws IOException {
return new rowIterator(up, firstKey);
}
public class rowIterator implements kelondroCloneableIterator<Entry> {
Iterator<byte[]> i;
boolean up;
byte[] fk;
int c;
public rowIterator(boolean up, byte[] firstKey) throws IOException {
this.up = up;
this.fk = firstKey;
this.i = index.keys(up, firstKey);
this.c = -1;
}
public kelondroCloneableIterator<Entry> clone(Object modifier) {
try {
return new rowIterator(up, fk);
} catch (IOException e) {
e.printStackTrace();
return null;
}
}
public boolean hasNext() {
return i.hasNext();
}
public Entry next() {
byte[] k = i.next();
assert k != null;
if (k == null) return null;
try {
this.c = index.geti(k);
} catch (IOException e) {
e.printStackTrace();
return null;
}
assert this.c >= 0;
if (this.c < 0) return null;
byte[] b = new byte[rowdef.objectsize];
if (table == null) {
// read from file
try {
file.get(this.c, b, 0);
} catch (IOException e) {
e.printStackTrace();
return null;
}
} else {
// compose from table and key
kelondroRow.Entry v = table.get(this.c, false);
assert v != null;
if (v == null) return null;
System.arraycopy(k, 0, b, 0, rowdef.primaryKeyLength);
System.arraycopy(v.bytes(), 0, b, rowdef.primaryKeyLength, taildef.objectsize);
}
return rowdef.newEntry(b);
}
public void remove() {
throw new UnsupportedOperationException("no remove in EcoTable");
}
}
public static kelondroIndex testTable(File f, String testentities, int testcase) throws IOException {
if (f.exists()) f.delete();
kelondroRow rowdef = new kelondroRow("byte[] a-4, byte[] b-4", kelondroNaturalOrder.naturalOrder, 0);
kelondroIndex tt = new kelondroEcoTable(f, rowdef, testcase, 100, 0);
byte[] b;
kelondroRow.Entry row = rowdef.newEntry();
for (int i = 0; i < testentities.length(); i++) {
b = kelondroTree.testWord(testentities.charAt(i));
row.setCol(0, b);
row.setCol(1, b);
tt.put(row);
}
return tt;
}
public static void bigtest(int elements, File testFile, int testcase) {
System.out.println("starting big test with " + elements + " elements:");
long start = System.currentTimeMillis();
String[] s = kelondroTree.permutations(elements);
kelondroIndex tt;
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], testcase);
if (kelondroTree.countElements(tt) != tt.size()) {
System.out.println("wrong size for " + s[i]);
}
tt.close();
for (int j = 0; j < s.length; j++) {
tt = testTable(testFile, s[i], testcase);
// delete by permutation j
for (int elt = 0; elt < s[j].length(); elt++) {
tt.remove(kelondroTree.testWord(s[j].charAt(elt)), false);
if (kelondroTree.countElements(tt) != tt.size()) {
System.out.println("ERROR! wrong size for probe tree " + s[i] + "; probe delete " + s[j] + "; position " + elt);
}
}
tt.close();
}
}
System.out.println("FINISHED test after " + ((System.currentTimeMillis() - start) / 1000) + " seconds.");
} catch (Exception e) {
e.printStackTrace();
System.out.println("TERMINATED");
}
}
public static void main(String[] args) {
// open a file, add one entry and exit
File f = new File(args[0]);
System.out.println("========= Testcase: no tail cache:");
bigtest(5, f, tailCacheDenyUsage);
System.out.println("========= Testcase: with tail cache:");
bigtest(5, f, tailCacheForceUsage);
/*
kelondroRow row = new kelondroRow("byte[] key-4, byte[] x-5", kelondroNaturalOrder.naturalOrder, 0);
try {
kelondroEcoTable t = new kelondroEcoTable(f, row);
kelondroRow.Entry entry = row.newEntry();
entry.setCol(0, "abcd".getBytes());
entry.setCol(1, "dummy".getBytes());
t.put(entry);
t.close();
} catch (IOException e) {
e.printStackTrace();
}
*/
}
}