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Sail implementation that stores data to disk using LMDB.
/*******************************************************************************
* Copyright (c) 2021 Eclipse RDF4J contributors.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Distribution License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/org/documents/edl-v10.php.
*
* SPDX-License-Identifier: BSD-3-Clause
*******************************************************************************/
package org.eclipse.rdf4j.sail.lmdb;
import static org.eclipse.rdf4j.sail.lmdb.LmdbUtil.E;
import static org.eclipse.rdf4j.sail.lmdb.LmdbUtil.openDatabase;
import static org.eclipse.rdf4j.sail.lmdb.LmdbUtil.readTransaction;
import static org.eclipse.rdf4j.sail.lmdb.LmdbUtil.transaction;
import static org.eclipse.rdf4j.sail.lmdb.Varint.readListUnsigned;
import static org.eclipse.rdf4j.sail.lmdb.Varint.writeUnsigned;
import static org.lwjgl.system.MemoryStack.stackPush;
import static org.lwjgl.system.MemoryUtil.NULL;
import static org.lwjgl.util.lmdb.LMDB.MDB_CREATE;
import static org.lwjgl.util.lmdb.LMDB.MDB_FIRST;
import static org.lwjgl.util.lmdb.LMDB.MDB_KEYEXIST;
import static org.lwjgl.util.lmdb.LMDB.MDB_LAST;
import static org.lwjgl.util.lmdb.LMDB.MDB_NEXT;
import static org.lwjgl.util.lmdb.LMDB.MDB_NOMETASYNC;
import static org.lwjgl.util.lmdb.LMDB.MDB_NOOVERWRITE;
import static org.lwjgl.util.lmdb.LMDB.MDB_NOSYNC;
import static org.lwjgl.util.lmdb.LMDB.MDB_NOTFOUND;
import static org.lwjgl.util.lmdb.LMDB.MDB_NOTLS;
import static org.lwjgl.util.lmdb.LMDB.MDB_PREV;
import static org.lwjgl.util.lmdb.LMDB.MDB_SET_RANGE;
import static org.lwjgl.util.lmdb.LMDB.MDB_SUCCESS;
import static org.lwjgl.util.lmdb.LMDB.mdb_cmp;
import static org.lwjgl.util.lmdb.LMDB.mdb_cursor_close;
import static org.lwjgl.util.lmdb.LMDB.mdb_cursor_get;
import static org.lwjgl.util.lmdb.LMDB.mdb_cursor_open;
import static org.lwjgl.util.lmdb.LMDB.mdb_dbi_close;
import static org.lwjgl.util.lmdb.LMDB.mdb_dbi_open;
import static org.lwjgl.util.lmdb.LMDB.mdb_del;
import static org.lwjgl.util.lmdb.LMDB.mdb_drop;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_close;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_create;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_info;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_open;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_set_mapsize;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_set_maxdbs;
import static org.lwjgl.util.lmdb.LMDB.mdb_env_set_maxreaders;
import static org.lwjgl.util.lmdb.LMDB.mdb_get;
import static org.lwjgl.util.lmdb.LMDB.mdb_put;
import static org.lwjgl.util.lmdb.LMDB.mdb_stat;
import static org.lwjgl.util.lmdb.LMDB.mdb_strerror;
import static org.lwjgl.util.lmdb.LMDB.mdb_txn_abort;
import static org.lwjgl.util.lmdb.LMDB.mdb_txn_begin;
import static org.lwjgl.util.lmdb.LMDB.mdb_txn_commit;
import java.io.Closeable;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.ByteBuffer;
import java.nio.IntBuffer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.concurrent.locks.StampedLock;
import java.util.function.Consumer;
import org.eclipse.rdf4j.sail.SailException;
import org.eclipse.rdf4j.sail.lmdb.TxnManager.Mode;
import org.eclipse.rdf4j.sail.lmdb.TxnManager.Txn;
import org.eclipse.rdf4j.sail.lmdb.TxnRecordCache.Record;
import org.eclipse.rdf4j.sail.lmdb.TxnRecordCache.RecordCacheIterator;
import org.eclipse.rdf4j.sail.lmdb.Varint.GroupMatcher;
import org.eclipse.rdf4j.sail.lmdb.config.LmdbStoreConfig;
import org.lwjgl.PointerBuffer;
import org.lwjgl.system.MemoryStack;
import org.lwjgl.util.lmdb.MDBEnvInfo;
import org.lwjgl.util.lmdb.MDBStat;
import org.lwjgl.util.lmdb.MDBVal;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* LMDB-based indexed storage and retrieval of RDF statements. TripleStore stores statements in the form of four long
* IDs. Each ID represent an RDF value that is stored in a {@link ValueStore}. The four IDs refer to the statement's
* subject, predicate, object and context. The ID 0 is used to represent the "null" context and doesn't map to
* an actual RDF value.
*/
@SuppressWarnings("deprecation")
class TripleStore implements Closeable {
/*-----------*
* Constants *
*-----------*/
// triples are represented by 4 varints for subject, predicate, object and context
static final int SUBJ_IDX = 0;
static final int PRED_IDX = 1;
static final int OBJ_IDX = 2;
static final int CONTEXT_IDX = 3;
static final int MAX_KEY_LENGTH = 4 * 9;
/**
* The default triple indexes.
*/
private static final String DEFAULT_INDEXES = "spoc,posc";
/**
* The file name for the properties file.
*/
private static final String PROPERTIES_FILE = "triples.prop";
/**
* The key used to store the triple store version in the properties file.
*/
private static final String VERSION_KEY = "version";
/**
* The key used to store the triple indexes specification that specifies which triple indexes exist.
*/
private static final String INDEXES_KEY = "triple-indexes";
/**
* The version number for the current triple store.
*
* - version 1: The first version with configurable triple indexes, a context field and a properties file.
*
*/
private static final int SCHEME_VERSION = 1;
/*-----------*
* Variables *
*-----------*/
private static final Logger logger = LoggerFactory.getLogger(TripleStore.class);
/**
* The directory that is used to store the index files.
*/
private final File dir;
/**
* Object containing meta-data for the triple store.
*/
private final Properties properties;
/**
* The list of triple indexes that are used to store and retrieve triples.
*/
private final List indexes = new ArrayList<>();
private long env;
private int contextsDbi;
private int pageSize;
private final boolean forceSync;
private final boolean autoGrow;
private long mapSize;
private long writeTxn;
private final TxnManager txnManager;
private final Pool pool = new Pool();
private TxnRecordCache recordCache = null;
static final Comparator COMPARATOR = new Comparator() {
@Override
public int compare(ByteBuffer b1, ByteBuffer b2) {
int b1Len = b1.remaining();
int b2Len = b2.remaining();
int diff = compareRegion(b1, b1.position(), b2, b2.position(), Math.min(b1Len, b2Len));
if (diff != 0) {
return diff;
}
return b1Len > b2Len ? 1 : -1;
}
public int compareRegion(ByteBuffer array1, int startIdx1, ByteBuffer array2, int startIdx2, int length) {
int result = 0;
for (int i = 0; result == 0 && i < length; i++) {
result = (array1.get(startIdx1 + i) & 0xff) - (array2.get(startIdx2 + i) & 0xff);
}
return result;
}
};
TripleStore(File dir, LmdbStoreConfig config) throws IOException, SailException {
this.dir = dir;
this.forceSync = config.getForceSync();
this.autoGrow = config.getAutoGrow();
// create directory if it not exists
this.dir.mkdirs();
try (MemoryStack stack = stackPush()) {
PointerBuffer pp = stack.mallocPointer(1);
E(mdb_env_create(pp));
env = pp.get(0);
}
E(mdb_env_set_maxdbs(env, 12));
E(mdb_env_set_maxreaders(env, 256));
// Open environment
int flags = MDB_NOTLS;
if (!forceSync) {
flags |= MDB_NOSYNC | MDB_NOMETASYNC;
}
E(mdb_env_open(env, this.dir.getAbsolutePath(), flags, 0664));
// open contexts database
contextsDbi = transaction(env, (stack, txn) -> {
String name = "contexts";
IntBuffer ip = stack.mallocInt(1);
if (mdb_dbi_open(txn, name, 0, ip) == MDB_NOTFOUND) {
E(mdb_dbi_open(txn, name, MDB_CREATE, ip));
}
return ip.get(0);
});
txnManager = new TxnManager(env, Mode.RESET);
File propFile = new File(this.dir, PROPERTIES_FILE);
String indexSpecStr = config.getTripleIndexes();
if (!propFile.exists()) {
// newly created lmdb store
properties = new Properties();
Set indexSpecs = parseIndexSpecList(indexSpecStr);
if (indexSpecs.isEmpty()) {
logger.debug("No indexes specified, using default indexes: {}", DEFAULT_INDEXES);
indexSpecStr = DEFAULT_INDEXES;
indexSpecs = parseIndexSpecList(indexSpecStr);
}
initIndexes(indexSpecs, config.getTripleDBSize());
} else {
// Read triple properties file and check format version number
properties = loadProperties(propFile);
checkVersion();
// Initialize existing indexes
Set indexSpecs = getIndexSpecs();
initIndexes(indexSpecs, config.getTripleDBSize());
// Compare the existing indexes with the requested indexes
Set reqIndexSpecs = parseIndexSpecList(indexSpecStr);
if (reqIndexSpecs.isEmpty()) {
// No indexes specified, use the existing ones
indexSpecStr = properties.getProperty(INDEXES_KEY);
} else if (!reqIndexSpecs.equals(indexSpecs)) {
// Set of indexes needs to be changed
reindex(indexSpecs, reqIndexSpecs);
}
}
if (!String.valueOf(SCHEME_VERSION).equals(properties.getProperty(VERSION_KEY))
|| !indexSpecStr.equals(properties.getProperty(INDEXES_KEY))) {
// Store up-to-date properties
properties.setProperty(VERSION_KEY, String.valueOf(SCHEME_VERSION));
properties.setProperty(INDEXES_KEY, indexSpecStr);
storeProperties(propFile);
}
}
private void checkVersion() throws SailException {
// Check version number
String versionStr = properties.getProperty(VERSION_KEY);
if (versionStr == null) {
logger.warn("{} missing in TripleStore's properties file", VERSION_KEY);
} else {
try {
int version = Integer.parseInt(versionStr);
if (version > SCHEME_VERSION) {
throw new SailException("Directory contains data that uses a newer data format");
}
} catch (NumberFormatException e) {
logger.warn("Malformed version number in TripleStore's properties file");
}
}
}
private Set getIndexSpecs() throws SailException {
String indexesStr = properties.getProperty(INDEXES_KEY);
if (indexesStr == null) {
throw new SailException(INDEXES_KEY + " missing in TripleStore's properties file");
}
Set indexSpecs = parseIndexSpecList(indexesStr);
if (indexSpecs.isEmpty()) {
throw new SailException("No " + INDEXES_KEY + " found in TripleStore's properties file");
}
return indexSpecs;
}
TxnManager getTxnManager() {
return txnManager;
}
/**
* Parses a comma/whitespace-separated list of index specifications. Index specifications are required to consists
* of 4 characters: 's', 'p', 'o' and 'c'.
*
* @param indexSpecStr A string like "spoc, pocs, cosp".
* @return A Set containing the parsed index specifications.
*/
private Set parseIndexSpecList(String indexSpecStr) throws SailException {
Set indexes = new HashSet<>();
if (indexSpecStr != null) {
StringTokenizer tok = new StringTokenizer(indexSpecStr, ", \t");
while (tok.hasMoreTokens()) {
String index = tok.nextToken().toLowerCase();
// sanity checks
if (index.length() != 4 || index.indexOf('s') == -1 || index.indexOf('p') == -1
|| index.indexOf('o') == -1 || index.indexOf('c') == -1) {
throw new SailException("invalid value '" + index + "' in index specification: " + indexSpecStr);
}
indexes.add(index);
}
}
return indexes;
}
private void initIndexes(Set indexSpecs, long tripleDbSize) throws IOException {
for (String fieldSeq : indexSpecs) {
logger.trace("Initializing index '{}'...", fieldSeq);
indexes.add(new TripleIndex(fieldSeq));
}
// initialize page size and set map size for env
readTransaction(env, (stack, txn) -> {
MDBStat stat = MDBStat.malloc(stack);
TripleIndex mainIndex = indexes.get(0);
mdb_stat(txn, mainIndex.getDB(true), stat);
boolean isEmpty = stat.ms_entries() == 0;
pageSize = stat.ms_psize();
// align map size with page size
long configMapSize = (tripleDbSize / pageSize) * pageSize;
if (isEmpty) {
// this is an empty db, use configured map size
mdb_env_set_mapsize(env, configMapSize);
}
MDBEnvInfo info = MDBEnvInfo.malloc(stack);
mdb_env_info(env, info);
mapSize = info.me_mapsize();
if (mapSize < configMapSize) {
// configured map size is larger than map size stored in env, increase map size
mdb_env_set_mapsize(env, configMapSize);
mapSize = configMapSize;
}
return null;
});
}
private void reindex(Set currentIndexSpecs, Set newIndexSpecs) throws IOException, SailException {
Map currentIndexes = new HashMap<>();
for (TripleIndex index : indexes) {
currentIndexes.put(new String(index.getFieldSeq()), index);
}
// Determine the set of newly added indexes and initialize these using an
// existing index as source
Set addedIndexSpecs = new HashSet<>(newIndexSpecs);
addedIndexSpecs.removeAll(currentIndexSpecs);
if (!addedIndexSpecs.isEmpty()) {
TripleIndex sourceIndex = indexes.get(0);
for (boolean explicit : new boolean[] { true, false }) {
transaction(env, (stack, txn) -> {
MDBVal keyValue = MDBVal.callocStack(stack);
ByteBuffer keyBuf = stack.malloc(MAX_KEY_LENGTH);
keyValue.mv_data(keyBuf);
MDBVal dataValue = MDBVal.callocStack(stack);
for (String fieldSeq : addedIndexSpecs) {
logger.debug("Initializing new index '{}'...", fieldSeq);
TripleIndex addedIndex = new TripleIndex(fieldSeq);
RecordIterator[] sourceIter = { null };
try {
sourceIter[0] = new LmdbRecordIterator(pool, sourceIndex, false, -1, -1, -1, -1,
explicit, txnManager.createTxn(txn));
RecordIterator it = sourceIter[0];
long[] quad;
while ((quad = it.next()) != null) {
keyBuf.clear();
addedIndex.toKey(keyBuf, quad[SUBJ_IDX], quad[PRED_IDX], quad[OBJ_IDX],
quad[CONTEXT_IDX]);
keyBuf.flip();
E(mdb_put(txn, addedIndex.getDB(explicit), keyValue, dataValue, 0));
}
} finally {
if (sourceIter[0] != null) {
sourceIter[0].close();
}
}
currentIndexes.put(fieldSeq, addedIndex);
}
return null;
});
}
logger.debug("New index(es) initialized");
}
// Determine the set of removed indexes
Set removedIndexSpecs = new HashSet<>(currentIndexSpecs);
removedIndexSpecs.removeAll(newIndexSpecs);
List removedIndexExceptions = new ArrayList<>();
transaction(env, (stack, txn) -> {
// Delete files for removed indexes
for (String fieldSeq : removedIndexSpecs) {
try {
TripleIndex removedIndex = currentIndexes.remove(fieldSeq);
removedIndex.destroy(txn);
logger.debug("Deleted file(s) for removed {} index", fieldSeq);
} catch (Throwable e) {
removedIndexExceptions.add(e);
}
}
return null;
});
if (!removedIndexExceptions.isEmpty()) {
throw new IOException(removedIndexExceptions.get(0));
}
// Update the indexes variable, using the specified index order
indexes.clear();
for (String fieldSeq : newIndexSpecs) {
indexes.add(currentIndexes.remove(fieldSeq));
}
}
@Override
public void close() throws IOException {
if (env != 0) {
endTransaction(false);
List caughtExceptions = new ArrayList<>();
for (TripleIndex index : indexes) {
try {
index.close();
} catch (Throwable e) {
logger.warn("Failed to close file for {} index", new String(index.getFieldSeq()));
caughtExceptions.add(e);
}
}
mdb_env_close(env);
env = 0;
if (!caughtExceptions.isEmpty()) {
throw new IOException(caughtExceptions.get(0));
}
}
}
/**
* Returns an iterator of all registered contexts.
*
* @param txn Active transaction
* @return All registered contexts
* @throws IOException
*/
public LmdbContextIdIterator getContexts(Txn txn) throws IOException {
return new LmdbContextIdIterator(this.pool, this.contextsDbi, txn);
}
/**
* If an index exists by context - use it, otherwise return null.
*
* @return All triples sorted by context or null if no context index exists
* @throws IOException
*/
public RecordIterator getAllTriplesSortedByContext(Txn txn) throws IOException {
for (TripleIndex index : indexes) {
if (index.getFieldSeq()[0] == 'c') {
// found a context-first index
return getTriplesUsingIndex(txn, -1, -1, -1, -1, true, index, false);
}
}
return null;
}
public RecordIterator getTriples(Txn txn, long subj, long pred, long obj, long context, boolean explicit)
throws IOException {
TripleIndex index = getBestIndex(subj, pred, obj, context);
// System.out.println("get triples: " + Arrays.asList(subj, pred, obj,context));
boolean doRangeSearch = index.getPatternScore(subj, pred, obj, context) > 0;
return getTriplesUsingIndex(txn, subj, pred, obj, context, explicit, index, doRangeSearch);
}
private RecordIterator getTriplesUsingIndex(Txn txn, long subj, long pred, long obj, long context,
boolean explicit, TripleIndex index, boolean rangeSearch) throws IOException {
return new LmdbRecordIterator(pool, index, rangeSearch, subj, pred, obj, context, explicit, txn);
}
/**
* Computes start key for a bucket by linear interpolation between a lower and an upper bound.
*
* @param fraction Value between 0 and 1
* @param lowerValues The lower bound
* @param upperValues The upper Bound
* @param startValues The interpolated values
*/
protected void bucketStart(double fraction, long[] lowerValues, long[] upperValues, long[] startValues) {
long diff = 0;
for (int i = 0; i < lowerValues.length; i++) {
if (diff == 0) {
// only interpolate the first value that is different
diff = upperValues[i] - lowerValues[i];
startValues[i] = diff == 0 ? lowerValues[i] : (long) (lowerValues[i] + diff * fraction);
} else {
// set rest of the values to 0
startValues[i] = 0;
}
}
}
/**
* Checks if any of ids is used and removes it from the collection.
*
* @param ids Collection with possibly removed IDs
* @throws IOException
*/
protected void filterUsedIds(Collection ids) throws IOException {
readTransaction(env, (stack, txn) -> {
MDBVal maxKey = MDBVal.malloc(stack);
ByteBuffer maxKeyBuf = stack.malloc(TripleStore.MAX_KEY_LENGTH);
MDBVal keyData = MDBVal.malloc(stack);
ByteBuffer keyBuf = stack.malloc(TripleStore.MAX_KEY_LENGTH);
MDBVal valueData = MDBVal.mallocStack(stack);
PointerBuffer pp = stack.mallocPointer(1);
// test contexts list if it contains the id
for (Iterator it = ids.iterator(); it.hasNext();) {
long id = it.next();
if (id < 0) {
it.remove();
continue;
}
keyBuf.clear();
Varint.writeUnsigned(keyBuf, id);
keyData.mv_data(keyBuf.flip());
if (mdb_get(txn, contextsDbi, keyData, valueData) == MDB_SUCCESS) {
it.remove();
}
}
// TODO currently this does not test for contexts (component == 3)
// because in most cases context indexes do not exist
for (int component = 0; component <= 2; component++) {
int c = component;
TripleIndex index = getBestIndex(component == 0 ? 1 : -1, component == 1 ? 1 : -1,
component == 2 ? 1 : -1, component == 3 ? 1 : -1);
boolean fullScan = index.getPatternScore(component == 0 ? 1 : -1, component == 1 ? 1 : -1,
component == 2 ? 1 : -1, component == 3 ? 1 : -1) == 0;
for (boolean explicit : new boolean[] { true, false }) {
int dbi = index.getDB(explicit);
long cursor = 0;
try {
E(mdb_cursor_open(txn, dbi, pp));
cursor = pp.get(0);
if (fullScan) {
long[] quad = new long[4];
int rc = mdb_cursor_get(cursor, keyData, valueData, MDB_FIRST);
while (rc == MDB_SUCCESS && !ids.isEmpty()) {
index.keyToQuad(keyData.mv_data(), quad);
ids.remove(quad[0]);
ids.remove(quad[1]);
ids.remove(quad[2]);
ids.remove(quad[3]);
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_NEXT);
}
} else {
for (Iterator it = ids.iterator(); it.hasNext();) {
long id = it.next();
if (id < 0) {
it.remove();
continue;
}
if (component != 2 && (id & 1) == 1) {
// id is a literal and can only appear in object position
continue;
}
long subj = c == 0 ? id : -1, pred = c == 1 ? id : -1,
obj = c == 2 ? id : -1, context = c == 3 ? id : -1;
GroupMatcher matcher = index.createMatcher(subj, pred, obj, context);
maxKeyBuf.clear();
index.getMaxKey(maxKeyBuf, subj, pred, obj, context);
maxKeyBuf.flip();
maxKey.mv_data(maxKeyBuf);
keyBuf.clear();
index.getMinKey(keyBuf, subj, pred, obj, context);
keyBuf.flip();
// set cursor to min key
keyData.mv_data(keyBuf);
int rc = mdb_cursor_get(cursor, keyData, valueData, MDB_SET_RANGE);
boolean exists = false;
while (!exists && rc == MDB_SUCCESS) {
if (mdb_cmp(txn, dbi, keyData, maxKey) > 0) {
// id was not found
break;
} else if (!matcher.matches(keyData.mv_data())) {
// value doesn't match search key/mask, fetch next value
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_NEXT);
} else {
exists = true;
}
}
if (exists) {
it.remove();
}
}
}
} finally {
if (cursor != 0) {
mdb_cursor_close(cursor);
}
}
}
}
return null;
});
}
protected double cardinality(long subj, long pred, long obj, long context) throws IOException {
TripleIndex index = getBestIndex(subj, pred, obj, context);
int relevantParts = index.getPatternScore(subj, pred, obj, context);
if (relevantParts == 0) {
// it's worthless to use the index, just retrieve all entries in the db
return txnManager.doWith((stack, txn) -> {
double cardinality = 0;
for (boolean explicit : new boolean[] { true, false }) {
int dbi = index.getDB(explicit);
MDBStat stat = MDBStat.mallocStack(stack);
mdb_stat(txn, dbi, stat);
cardinality += (double) stat.ms_entries();
}
return cardinality;
});
}
return txnManager.doWith((stack, txn) -> {
final Statistics s = pool.getStatistics();
try {
MDBVal maxKey = MDBVal.malloc(stack);
ByteBuffer maxKeyBuf = stack.malloc(TripleStore.MAX_KEY_LENGTH);
index.getMaxKey(maxKeyBuf, subj, pred, obj, context);
maxKeyBuf.flip();
maxKey.mv_data(maxKeyBuf);
PointerBuffer pp = stack.mallocPointer(1);
MDBVal keyData = MDBVal.mallocStack(stack);
ByteBuffer keyBuf = stack.malloc(TripleStore.MAX_KEY_LENGTH);
MDBVal valueData = MDBVal.mallocStack(stack);
double cardinality = 0;
for (boolean explicit : new boolean[] { true, false }) {
Arrays.fill(s.avgRowsPerValue, 1.0);
Arrays.fill(s.avgRowsPerValueCounts, 0);
keyBuf.clear();
index.getMinKey(keyBuf, subj, pred, obj, context);
keyBuf.flip();
int dbi = index.getDB(explicit);
int pos = 0;
long cursor = 0;
try {
E(mdb_cursor_open(txn, dbi, pp));
cursor = pp.get(0);
// set cursor to min key
keyData.mv_data(keyBuf);
int rc = mdb_cursor_get(cursor, keyData, valueData, MDB_SET_RANGE);
if (rc != MDB_SUCCESS || mdb_cmp(txn, dbi, keyData, maxKey) >= 0) {
break;
} else {
Varint.readListUnsigned(keyData.mv_data(), s.minValues);
}
// set cursor to max key
keyData.mv_data(maxKeyBuf);
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_SET_RANGE);
if (rc != MDB_SUCCESS) {
// directly go to last value
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_LAST);
} else {
// go to previous value of selected key
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_PREV);
}
if (rc == MDB_SUCCESS) {
Varint.readListUnsigned(keyData.mv_data(), s.maxValues);
// this is required to correctly estimate the range size at a later point
s.startValues[s.MAX_BUCKETS] = s.maxValues;
} else {
break;
}
long allSamplesCount = 0;
int bucket = 0;
boolean endOfRange = false;
for (; bucket < s.MAX_BUCKETS && !endOfRange; bucket++) {
if (bucket != 0) {
bucketStart((double) bucket / s.MAX_BUCKETS, s.minValues, s.maxValues, s.values);
keyBuf.clear();
Varint.writeListUnsigned(keyBuf, s.values);
keyBuf.flip();
}
// this is the min key for the first iteration
keyData.mv_data(keyBuf);
int currentSamplesCount = 0;
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_SET_RANGE);
while (rc == MDB_SUCCESS && currentSamplesCount < s.MAX_SAMPLES_PER_BUCKET) {
if (mdb_cmp(txn, dbi, keyData, maxKey) >= 0) {
endOfRange = true;
break;
} else {
allSamplesCount++;
currentSamplesCount++;
System.arraycopy(s.values, 0, s.lastValues[bucket], 0, s.values.length);
Varint.readListUnsigned(keyData.mv_data(), s.values);
if (currentSamplesCount == 1) {
Arrays.fill(s.counts, 1);
System.arraycopy(s.values, 0, s.startValues[bucket], 0, s.values.length);
} else {
for (int i = 0; i < s.values.length; i++) {
if (s.values[i] == s.lastValues[bucket][i]) {
s.counts[i]++;
} else {
long diff = s.values[i] - s.lastValues[bucket][i];
s.avgRowsPerValueCounts[i]++;
s.avgRowsPerValue[i] = (s.avgRowsPerValue[i]
* (s.avgRowsPerValueCounts[i] - 1) +
(double) s.counts[i] / diff) / s.avgRowsPerValueCounts[i];
s.counts[i] = 0;
}
}
}
rc = mdb_cursor_get(cursor, keyData, valueData, MDB_NEXT);
if (rc != MDB_SUCCESS) {
// no more elements are available
endOfRange = true;
}
}
}
}
// at least the seen samples must be counted
cardinality += allSamplesCount;
// the actual number of buckets (bucket - 1 "real" buckets and one for the last element within
// the range)
int buckets = bucket;
for (bucket = 1; bucket < buckets; bucket++) {
// find first element that has been changed
pos = 0;
while (pos < s.lastValues[bucket].length
&& s.startValues[bucket][pos] == s.lastValues[bucket - 1][pos]) {
pos++;
}
if (pos < s.lastValues[bucket].length) {
// this may be < 0 if two groups are overlapping
long diffBetweenGroups = Math
.max(s.startValues[bucket][pos] - s.lastValues[bucket - 1][pos], 0);
// estimate number of elements between last element of previous bucket and first element
// of current bucket
cardinality += s.avgRowsPerValue[pos] * diffBetweenGroups;
}
}
} finally {
if (cursor != 0) {
mdb_cursor_close(cursor);
}
}
}
return cardinality;
} finally {
pool.free(s);
}
});
}
protected TripleIndex getBestIndex(long subj, long pred, long obj, long context) {
int bestScore = -1;
TripleIndex bestIndex = null;
for (TripleIndex index : indexes) {
int score = index.getPatternScore(subj, pred, obj, context);
if (score > bestScore) {
bestScore = score;
bestIndex = index;
}
}
return bestIndex;
}
private boolean requiresResize() {
if (autoGrow) {
return LmdbUtil.requiresResize(mapSize, pageSize, writeTxn, 0);
} else {
return false;
}
}
public boolean storeTriple(long subj, long pred, long obj, long context, boolean explicit) throws IOException {
TripleIndex mainIndex = indexes.get(0);
boolean stAdded;
try (MemoryStack stack = MemoryStack.stackPush()) {
MDBVal keyVal = MDBVal.malloc(stack);
// use calloc to get an empty data value
MDBVal dataVal = MDBVal.calloc(stack);
ByteBuffer keyBuf = stack.malloc(MAX_KEY_LENGTH);
mainIndex.toKey(keyBuf, subj, pred, obj, context);
keyBuf.flip();
keyVal.mv_data(keyBuf);
if (recordCache == null) {
if (requiresResize()) {
// map is full, resize required
recordCache = new TxnRecordCache(dir);
logger.debug("resize of map size {} required while adding - initialize record cache", mapSize);
}
}
if (recordCache != null) {
long quad[] = new long[] { subj, pred, obj, context };
if (explicit) {
// remove implicit statement
recordCache.removeRecord(quad, false);
}
// put record in cache and return immediately
return recordCache.storeRecord(quad, explicit);
}
int rc = mdb_put(writeTxn, mainIndex.getDB(explicit), keyVal, dataVal, MDB_NOOVERWRITE);
if (rc != MDB_SUCCESS && rc != MDB_KEYEXIST) {
throw new IOException(mdb_strerror(rc));
}
stAdded = rc == MDB_SUCCESS;
boolean foundImplicit = false;
if (explicit && stAdded) {
foundImplicit = mdb_del(writeTxn, mainIndex.getDB(false), keyVal, dataVal) == MDB_SUCCESS;
}
if (stAdded) {
for (int i = 1; i < indexes.size(); i++) {
TripleIndex index = indexes.get(i);
keyBuf.clear();
index.toKey(keyBuf, subj, pred, obj, context);
keyBuf.flip();
// update buffer positions in MDBVal
keyVal.mv_data(keyBuf);
if (foundImplicit) {
E(mdb_del(writeTxn, mainIndex.getDB(false), keyVal, dataVal));
}
E(mdb_put(writeTxn, index.getDB(explicit), keyVal, dataVal, 0));
}
if (stAdded) {
incrementContext(stack, context);
}
}
}
return stAdded;
}
private void incrementContext(MemoryStack stack, long context) throws IOException {
try {
stack.push();
MDBVal idVal = MDBVal.calloc(stack);
ByteBuffer bb = stack.malloc(1 + Long.BYTES);
Varint.writeUnsigned(bb, context);
bb.flip();
idVal.mv_data(bb);
MDBVal dataVal = MDBVal.calloc(stack);
long newCount = 1;
if (mdb_get(writeTxn, contextsDbi, idVal, dataVal) == MDB_SUCCESS) {
// update count
newCount = Varint.readUnsigned(dataVal.mv_data()) + 1;
}
// write count
ByteBuffer countBb = stack.malloc(Varint.calcLengthUnsigned(newCount));
Varint.writeUnsigned(countBb, newCount);
dataVal.mv_data(countBb.flip());
E(mdb_put(writeTxn, contextsDbi, idVal, dataVal, 0));
} finally {
stack.pop();
}
}
private boolean decrementContext(MemoryStack stack, long context) throws IOException {
try {
stack.push();
MDBVal idVal = MDBVal.calloc(stack);
ByteBuffer bb = stack.malloc(1 + Long.BYTES);
Varint.writeUnsigned(bb, context);
bb.flip();
idVal.mv_data(bb);
MDBVal dataVal = MDBVal.calloc(stack);
if (mdb_get(writeTxn, contextsDbi, idVal, dataVal) == MDB_SUCCESS) {
// update count
long newCount = Varint.readUnsigned(dataVal.mv_data()) - 1;
if (newCount <= 0) {
E(mdb_del(writeTxn, contextsDbi, idVal, null));
return true;
} else {
// write count
ByteBuffer countBb = stack.malloc(Varint.calcLengthUnsigned(newCount));
Varint.writeUnsigned(countBb, newCount);
dataVal.mv_data(countBb.flip());
E(mdb_put(writeTxn, contextsDbi, idVal, dataVal, 0));
}
}
return false;
} finally {
stack.pop();
}
}
/**
* @param subj The subject for the pattern, or -1 for a wildcard.
* @param pred The predicate for the pattern, or -1 for a wildcard.
* @param obj The object for the pattern, or -1 for a wildcard.
* @param context The context for the pattern, or -1 for a wildcard.
* @param explicit Flag indicating whether explicit or inferred statements should be removed; true removes
* explicit statements that match the pattern, false removes inferred statements that match
* the pattern.
* @param handler Function that gets notified about each deleted quad
* @throws IOException
*/
public void removeTriplesByContext(long subj, long pred, long obj, long context,
boolean explicit, Consumer handler) throws IOException {
RecordIterator records = getTriples(txnManager.createTxn(writeTxn), subj, pred, obj, context, explicit);
removeTriples(records, explicit, handler);
}
public void removeTriples(RecordIterator it, boolean explicit, Consumer handler) throws IOException {
try (it; MemoryStack stack = MemoryStack.stackPush()) {
MDBVal keyValue = MDBVal.callocStack(stack);
ByteBuffer keyBuf = stack.malloc(MAX_KEY_LENGTH);
long[] quad;
while ((quad = it.next()) != null) {
if (recordCache == null) {
if (requiresResize()) {
// map is full, resize required
recordCache = new TxnRecordCache(dir);
logger.debug("resize of map size {} required while removing - initialize record cache",
mapSize);
}
}
if (recordCache != null) {
recordCache.removeRecord(quad, explicit);
handler.accept(quad);
continue;
}
for (TripleIndex index : indexes) {
keyBuf.clear();
index.toKey(keyBuf, quad[SUBJ_IDX], quad[PRED_IDX], quad[OBJ_IDX], quad[CONTEXT_IDX]);
keyBuf.flip();
// update buffer positions in MDBVal
keyValue.mv_data(keyBuf);
E(mdb_del(writeTxn, index.getDB(explicit), keyValue, null));
}
decrementContext(stack, quad[CONTEXT_IDX]);
handler.accept(quad);
}
}
}
protected void updateFromCache() throws IOException {
recordCache.commit();
for (boolean explicit : new boolean[] { true, false }) {
RecordCacheIterator it = recordCache.getRecords(explicit);
try (MemoryStack stack = MemoryStack.stackPush()) {
PointerBuffer pp = stack.mallocPointer(1);
MDBVal keyVal = MDBVal.mallocStack(stack);
// use calloc to get an empty data value
MDBVal dataVal = MDBVal.callocStack(stack);
ByteBuffer keyBuf = stack.malloc(MAX_KEY_LENGTH);
Record r;
while ((r = it.next()) != null) {
if (requiresResize()) {
// resize map if required
E(mdb_txn_commit(writeTxn));
mapSize = LmdbUtil.autoGrowMapSize(mapSize, pageSize, 0);
E(mdb_env_set_mapsize(env, mapSize));
logger.debug("resized map to {}", mapSize);
E(mdb_txn_begin(env, NULL, 0, pp));
writeTxn = pp.get(0);
}
for (int i = 0; i < indexes.size(); i++) {
TripleIndex index = indexes.get(i);
keyBuf.clear();
index.toKey(keyBuf, r.quad[0], r.quad[1], r.quad[2], r.quad[3]);
keyBuf.flip();
// update buffer positions in MDBVal
keyVal.mv_data(keyBuf);
if (r.add) {
E(mdb_put(writeTxn, index.getDB(explicit), keyVal, dataVal, 0));
} else {
E(mdb_del(writeTxn, index.getDB(explicit), keyVal, null));
}
}
}
}
}
recordCache.close();
}
public void startTransaction() throws IOException {
try (MemoryStack stack = stackPush()) {
PointerBuffer pp = stack.mallocPointer(1);
E(mdb_txn_begin(env, NULL, 0, pp));
writeTxn = pp.get(0);
}
}
/**
* Closes the snapshot and the DB iterator if any was opened in the current transaction
*/
void endTransaction(boolean commit) throws IOException {
if (writeTxn != 0) {
try {
if (commit) {
try {
E(mdb_txn_commit(writeTxn));
if (recordCache != null) {
StampedLock lock = txnManager.lock();
long stamp = lock.writeLock();
try {
txnManager.deactivate();
mapSize = LmdbUtil.autoGrowMapSize(mapSize, pageSize, 0);
E(mdb_env_set_mapsize(env, mapSize));
logger.debug("resized map to {}", mapSize);
// restart write transaction
try (MemoryStack stack = stackPush()) {
PointerBuffer pp = stack.mallocPointer(1);
mdb_txn_begin(env, NULL, 0, pp);
writeTxn = pp.get(0);
}
updateFromCache();
// finally, commit write transaction
E(mdb_txn_commit(writeTxn));
} finally {
recordCache = null;
try {
txnManager.activate();
} finally {
lock.unlockWrite(stamp);
}
}
} else {
// invalidate open read transaction so that they are not re-used
// otherwise iterators won't see the updated data
txnManager.reset();
}
} catch (IOException e) {
// abort transaction if exception occurred while committing
mdb_txn_abort(writeTxn);
throw e;
}
} else {
mdb_txn_abort(writeTxn);
}
} finally {
writeTxn = 0;
// ensure that record cache is always reset
if (recordCache != null) {
try {
recordCache.close();
} finally {
recordCache = null;
}
}
}
}
}
public void commit() throws IOException {
endTransaction(true);
}
public void rollback() throws IOException {
endTransaction(false);
}
private Properties loadProperties(File propFile) throws IOException {
try (InputStream in = new FileInputStream(propFile)) {
Properties properties = new Properties();
properties.load(in);
return properties;
}
}
private void storeProperties(File propFile) throws IOException {
try (OutputStream out = new FileOutputStream(propFile)) {
properties.store(out, "triple indexes meta-data, DO NOT EDIT!");
}
}
class TripleIndex {
private final char[] fieldSeq;
private final int dbiExplicit, dbiInferred;
private final int[] indexMap;
public TripleIndex(String fieldSeq) throws IOException {
this.fieldSeq = fieldSeq.toCharArray();
this.indexMap = getIndexes(this.fieldSeq);
// open database and use native sort order without comparator
dbiExplicit = openDatabase(env, fieldSeq, MDB_CREATE, null);
dbiInferred = openDatabase(env, fieldSeq + "-inf", MDB_CREATE, null);
}
public char[] getFieldSeq() {
return fieldSeq;
}
public int getDB(boolean explicit) {
return explicit ? dbiExplicit : dbiInferred;
}
protected int[] getIndexes(char[] fieldSeq) {
int[] indexes = new int[fieldSeq.length];
for (int i = 0; i < fieldSeq.length; i++) {
char field = fieldSeq[i];
int fieldIdx;
switch (field) {
case 's':
fieldIdx = SUBJ_IDX;
break;
case 'p':
fieldIdx = PRED_IDX;
break;
case 'o':
fieldIdx = OBJ_IDX;
break;
case 'c':
fieldIdx = CONTEXT_IDX;
break;
default:
throw new IllegalArgumentException(
"invalid character '" + field + "' in field sequence: " + new String(fieldSeq));
}
indexes[i] = fieldIdx;
}
return indexes;
}
/**
* Determines the 'score' of this index on the supplied pattern of subject, predicate, object and context IDs.
* The higher the score, the better the index is suited for matching the pattern. Lowest score is 0, which means
* that the index will perform a sequential scan.
*/
public int getPatternScore(long subj, long pred, long obj, long context) {
int score = 0;
for (char field : fieldSeq) {
switch (field) {
case 's':
if (subj >= 0) {
score++;
} else {
return score;
}
break;
case 'p':
if (pred >= 0) {
score++;
} else {
return score;
}
break;
case 'o':
if (obj >= 0) {
score++;
} else {
return score;
}
break;
case 'c':
if (context >= 0) {
score++;
} else {
return score;
}
break;
default:
throw new RuntimeException("invalid character '" + field + "' in field sequence: "
+ new String(fieldSeq));
}
}
return score;
}
void getMinKey(ByteBuffer bb, long subj, long pred, long obj, long context) {
subj = subj <= 0 ? 0 : subj;
pred = pred <= 0 ? 0 : pred;
obj = obj <= 0 ? 0 : obj;
context = context <= 0 ? 0 : context;
toKey(bb, subj, pred, obj, context);
}
void getMaxKey(ByteBuffer bb, long subj, long pred, long obj, long context) {
subj = subj <= 0 ? Long.MAX_VALUE : subj;
pred = pred <= 0 ? Long.MAX_VALUE : pred;
obj = obj <= 0 ? Long.MAX_VALUE : obj;
context = context < 0 ? Long.MAX_VALUE : context;
toKey(bb, subj, pred, obj, context);
}
GroupMatcher createMatcher(long subj, long pred, long obj, long context) {
ByteBuffer bb = ByteBuffer.allocate(TripleStore.MAX_KEY_LENGTH);
toKey(bb, subj == -1 ? 0 : subj, pred == -1 ? 0 : pred, obj == -1 ? 0 : obj, context == -1 ? 0 : context);
bb.flip();
boolean[] shouldMatch = new boolean[4];
for (int i = 0; i < fieldSeq.length; i++) {
switch (fieldSeq[i]) {
case 's':
shouldMatch[i] = subj > 0;
break;
case 'p':
shouldMatch[i] = pred > 0;
break;
case 'o':
shouldMatch[i] = obj > 0;
break;
case 'c':
shouldMatch[i] = context >= 0;
break;
}
}
return new GroupMatcher(bb, shouldMatch);
}
void toKey(ByteBuffer bb, long subj, long pred, long obj, long context) {
for (int i = 0; i < fieldSeq.length; i++) {
switch (fieldSeq[i]) {
case 's':
writeUnsigned(bb, subj);
break;
case 'p':
writeUnsigned(bb, pred);
break;
case 'o':
writeUnsigned(bb, obj);
break;
case 'c':
writeUnsigned(bb, context);
break;
}
}
}
void keyToQuad(ByteBuffer key, long[] quad) {
// directly use index map to read values in to correct positions
readListUnsigned(key, indexMap, quad);
}
@Override
public String toString() {
return new String(getFieldSeq());
}
void close() {
mdb_dbi_close(env, dbiExplicit);
mdb_dbi_close(env, dbiInferred);
pool.close();
}
void clear(long txn) {
mdb_drop(txn, dbiExplicit, false);
mdb_drop(txn, dbiInferred, false);
}
void destroy(long txn) {
mdb_drop(txn, dbiExplicit, true);
mdb_drop(txn, dbiInferred, true);
}
}
}
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