com.bigdata.rdf.lexicon.BlobsIndexHelper Maven / Gradle / Ivy
/**
Copyright (C) SYSTAP, LLC DBA Blazegraph 2006-2016. All rights reserved.
Contact:
SYSTAP, LLC DBA Blazegraph
2501 Calvert ST NW #106
Washington, DC 20008
[email protected]
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; version 2 of the License.
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
*/
/*
* Created on Jun 6, 2011
*/
package com.bigdata.rdf.lexicon;
import java.io.IOException;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.log4j.Logger;
import org.openrdf.model.BNode;
import org.openrdf.model.Value;
import com.bigdata.btree.IIndex;
import com.bigdata.btree.IRangeQuery;
import com.bigdata.btree.ITuple;
import com.bigdata.btree.ITupleIterator;
import com.bigdata.btree.keys.IKeyBuilder;
import com.bigdata.btree.keys.KVO;
import com.bigdata.btree.keys.KeyBuilder;
import com.bigdata.btree.keys.SuccessorUtil;
import com.bigdata.io.ByteArrayBuffer;
import com.bigdata.io.DataOutputBuffer;
import com.bigdata.rdf.internal.INonInlineExtensionCodes;
import com.bigdata.rdf.internal.IV;
import com.bigdata.rdf.internal.VTE;
import com.bigdata.rdf.internal.impl.BlobIV;
import com.bigdata.rdf.model.BigdataValue;
import com.bigdata.rdf.model.BigdataValueFactory;
import com.bigdata.rdf.model.BigdataValueSerializer;
import com.bigdata.rdf.store.AbstractTripleStore;
import com.bigdata.util.Bytes;
import com.bigdata.util.BytesUtil;
/**
* Helper class for operations on the BLOBS index.
*/
public class BlobsIndexHelper {
private static final Logger log = Logger.getLogger(BlobsIndexHelper.class);
public static final transient int SIZEOF_HASH = Bytes.SIZEOF_INT;
/**
* The size of the hash collision counter.
*/
public static final transient int SIZEOF_COUNTER = Bytes.SIZEOF_SHORT;
/** The maximum value of the hash collision counter (unsigned short). */
public static final transient int MAX_COUNTER = ((1 << 16) - 1);
/** The offset at which the counter occurs in the key. */
public static final transient int OFFSET_COUNTER = 1/* flags */+ 1/* extension */+ SIZEOF_HASH /* hashCode */;
/** The size of a prefix key (a key without a hash collision counter). */
public static final transient int SIZEOF_PREFIX_KEY = OFFSET_COUNTER;
/**
* The size of a key in the TERMS index.
*
* Note: The key is size is ONE (1) byte for the [flags] byte, ONE (1) for
* the extension byte (which describes what kind of non-inline IV this is),
* FOUR (4) bytes for the hash code, plus a TWO (2) byte counter (to break
* ties within a collision bucket).
*
* Note: The counter size was increased when the design purpose of this
* index was changed to handling large RDF {@link Value}s only. In practice,
* the hash codes of the RDF {@link Value} are well distributed and
* collisions within a hash bucket (same hash code) are rare. A ONE (1) byte
* counter is probably all the distinctions that we could require and
* permits up to 256 hash collisions. However, when operating in scale-out
* the TWO (2) byte (aka short) counter provides additional confidence that
* hash collisions will not result in a hash bucket overflow. Given that the
* terms index will be used only with larger RDF {@link Value}s and the
* necessity for the "extension" byte, it seems a small added cost to have
* the TWO (2) byte counter and provides additional peace of mind. However,
* note that scanning large collision buckets is expensive. But by allowing
* for large collision buckets, we will pay that cost only when the hash
* codes have an unusual distribution for some specific value.
*
* The total key size is only 8 bytes. Since only large values are being
* stored under the TERMS index, they will always be written as raw records
* on the backing store. This means that we have an 8 byte key paired with
* an 8 byte address. That allows for practical branching factors of between
* 512 and 1024 to obtain an expected average page sizes of ~ 8k (after
* prefix compression, etc.).
*/
public static final transient int TERMS_INDEX_KEY_SIZE = 1 + 1
+ SIZEOF_HASH + SIZEOF_COUNTER;
/**
* Arbitrary threshold for the collision counter for a given hash code at
* which we will log @ WARN. This provides notice when there are large hash
* collision buckets which can effect performance.
*/
public static final transient int LOG_WARN_COUNTER_THRESHOLD = 127;
/**
* Used to signal that the {@link Value} was not found on a read-only
* request.
*/
public static final transient int NOT_FOUND = Integer.MIN_VALUE;
/**
* Generate the sort keys for {@link BigdataValue}s to be represented as
* {@link BlobIV}s. The sort key is formed from the {@link VTE} of the
* {@link BigdataValue} followed by the hashCode of the {@link BigdataValue}
* . Note that the sort key formed in this manner is only a prefix key for
* the TERMS index. The fully formed key also includes a counter to breaks
* ties when the sort key formed from {@link VTE} and hashCode results in a
* collision (different {@link BigdataValue}s having the same prefix key).
*
* @param valSer
* The object used to generate the values to be written onto the
* index.
* @param terms
* The terms whose sort keys will be generated.
* @param numTerms
* The #of terms in that array.
*
* @return An array of correlated key-value-object tuples.
*/
@SuppressWarnings("unchecked")
public KVO[] generateKVOs(
final BigdataValueSerializer valSer,
final BigdataValue[] terms, final int numTerms) {
if (valSer == null)
throw new IllegalArgumentException();
if (terms == null)
throw new IllegalArgumentException();
if (numTerms <= 0 || numTerms > terms.length)
throw new IllegalArgumentException();
final KVO[] a = new KVO[numTerms];
final IKeyBuilder keyBuilder = newKeyBuilder();
final ByteArrayBuffer tmp = new ByteArrayBuffer();
final DataOutputBuffer out = new DataOutputBuffer();
try {
for (int i = 0; i < numTerms; i++) {
final BigdataValue term = terms[i];
final VTE vte = VTE.valueOf(term);
final int hashCode = term.hashCode();
final byte[] key = makePrefixKey(keyBuilder.reset(), vte,
hashCode);
final byte[] val = valSer.serialize(term, out.reset(), tmp);
a[i] = new KVO(key, val, term);
}
} finally {
try {
/*
* Note: Both the outer and inner try/catch are just to please
* find bugs. DataOutputStream.close() is a NOP.
*/
out.close();
} catch (IOException ex) {
throw new RuntimeException(ex);
}
}
return a;
}
/**
* Resolve an existing record in the TERMS index and insert the record if
* none is found.
*
* @param termsIndex
* The TERMS index.
* @param readOnly
* true iff the operation is read only.
* @param keyBuilder
* The buffer will be reset as necessary.
* @param baseKey
* The base key for the hash code (without the counter suffix).
* @param val
* The (serialized and compressed) RDF Value.
* @param tmp
* The buffer used to format the toKey (optional). A new
* byte[] will be allocated if this is null, but the
* same byte[] can be reused for multiple invocations. The buffer
* MUST be dimensioned to
* {@link BlobsIndexHelper#SIZEOF_PREFIX_KEY}.
* @param bucketSize
* The size of the collision bucket is reported as a side-effect
* (optional).
*
* @return The collision counter for the key under which the {@link Value}
* was found (if pre-existing), the collision counter assigned to
* the {@link Value} iff the value was not found and the operation
* permitted writes -or- {@link Integer#MIN_VALUE} iff the
* {@link Value} is not in the index and the operation is read-only.
*
* @throws CollisionBucketSizeException
* if an attempt is made to insert a {@link Value} into a
* collision bucket which is full.
*/
public int resolveOrAddValue(final IIndex termsIndex,
final boolean readOnly, final IKeyBuilder keyBuilder,
final byte[] baseKey, final byte[] val, final byte[] tmp,
final AtomicInteger bucketSize) {
assert baseKey.length == BlobsIndexHelper.SIZEOF_PREFIX_KEY : "Expecting "
+ BlobsIndexHelper.SIZEOF_PREFIX_KEY
+ " bytes, not "
+ baseKey.length;
/*
* This is the fixed length hash code prefix. When a collision
* exists we can either append a counter -or- use more bits from the
* prefix. An extensible hash index works by progressively
* increasing the #of bits from the hash code which are used to
* create a distinction in the index. Records with identical hash
* values are stored in an (unordered, and possibly chained) bucket.
* We can approximate this by using N-bits of the hash code for the
* key and then increasing the #of bits in the key when there is a
* hash collision. Unless a hash function is used which has
* sufficient bits available to ensure that there are no collisions,
* we may be forced eventually to append a counter to impose a
* distinction among records which are hash identical but whose
* values differ.
*
* In the case of a hash collision, we can determine the records
* which have already collided using the fast range count between
* the hash code key and the fixed length successor of that key. We
* can create a guaranteed distinct key by creating a BigInteger
* whose values is (#collisions+1) and appending it to the key. This
* approach will give us keys whose byte length increases slowly as
* the #of collisions grows (though these might not be the minimum
* length keys - depending on how we are encoding the BigInteger in
* the key.)
*
* When we have a hash collision, we first need to scan all of the
* collision records and make sure that none of those records has
* the same value as the given record. This is done using the fixed
* length successor of the hash code key as the exclusive upper
* bound of a key range scan. Each record associated with a tuple in
* that key range must be compared for equality with the given
* record to decide whether or not the given record already exists
* in the index.
*
* The fromKey is strictly LT any full key for the hash code of this
* val but strictly GT any key have a hash code LT the hash code of
* this val.
*/
final byte[] fromKey = baseKey;
// key strictly LT any successor of the hash code of this val.
final byte[] toKey = makeToKey(fromKey, tmp);
// fast range count. this tells us how many collisions there are.
// this is an exact collision count since we are not deleting tuples
// from the TERMS index.
final long rangeCount = termsIndex.rangeCount(fromKey, toKey);
if (bucketSize != null)
bucketSize.set((int) rangeCount);
if (rangeCount == 0 && readOnly) {
// Fast path.
return NOT_FOUND;
}
if (rangeCount >= MAX_COUNTER) {
/*
* Impose a hard limit on the #of hash collisions we will accept in
* this utility.
*/
throw new CollisionBucketSizeException(rangeCount);
}
// // Force range count into (signed) byte
// final byte counter = (byte) rangeCount;
if (rangeCount == 0) {
assert !readOnly;
/*
* This is the first time we have observed a Value which
* generates this hash code, so append a [short] ZERO (0) to
* generate the actual key and then insert the Value into the
* index. Since there is nothing in the index for this hash
* code, no collision is possible and we do not need to test the
* index for the value before inserting the value into the
* index.
*/
final byte[] key = makeKey(keyBuilder.reset(), baseKey,
(int) rangeCount);
if (termsIndex.insert(key, val) != null) {
throw new AssertionError();
}
return (int) rangeCount;
}
/*
* Iterator over that key range
*
* Note: We need to visit the keys in case we have a match since we will
* need to return that key (it will become wrapped as an IV).
*
* Note: We need to visit the values so we can test tuples within the
* same collision bucket (same key up to the counter) to determine
* whether or not the Value is in fact the same.
*/
final ITupleIterator itr = termsIndex
.rangeIterator(fromKey, toKey, 0/* capacity */,
IRangeQuery.KEYS | IRangeQuery.VALS, null/* filter */);
while(itr.hasNext()) {
final ITuple tuple = itr.next();
if (tuple.isNull()) {
// Can not match a NullIV.
continue;
}
final ByteArrayBuffer tb = tuple.getValueBuffer();
// final byte[] tmp2 = tuple.getValue();
//
// // Note: Compares the compressed values ;-)
// if(BytesUtil.bytesEqual(val, tmp2)) {
// compare without materializing the tuple's value
if (0 == BytesUtil.compareBytesWithLenAndOffset(
0/* aoff */, val.length/* alen */, val,//
0/* boff */, tb.limit()/* blen */, tb.array()/* b */
)) {
// Already in the index.
final short asFoundCounter = KeyBuilder.decodeShort(tuple
.getKeyBuffer().array(), OFFSET_COUNTER);
return asFoundCounter;
}
}
if (readOnly) {
// Not found.
return NOT_FOUND;
}
/*
* Hash collision.
*/
final byte[] key = makeKey(keyBuilder.reset(), baseKey,
(int) rangeCount);
// Insert into the index.
if (termsIndex.insert(key, val) != null) {
throw new AssertionError();
}
if (rangeCount >= LOG_WARN_COUNTER_THRESHOLD) {
log.warn("Collision: hashCode=" + BytesUtil.toString(key)
+ ", collisionBucketSize=" + rangeCount);
}
return (int) rangeCount;
}
/**
* Add an entry for a {@link BNode} to the TERMS index (do NOT use when told
* blank node semantics apply).
*
* All {@link BNode}s entered by this method are distinct regardless of
* their {@link BNode#getID()}. Since blank nodes can not be unified with
* the TERMS index (unless we are using told blank node semantics) we simply
* add another entry for the caller's {@link BNode} and return the key for
* that entry which will be wrapped as an {@link IV}. That entry will be
* made distinct from all other entries for the same {@link VTE} and
* hashCode by appending the current collision counter (which is just the
* range count).
*
* @param termsIndex
* The TERMS index.
* @param keyBuilder
* The buffer will be reset as necessary.
* @param baseKey
* The base key for the hash code (without the counter suffix).
* @param val
* The (serialized and compressed) RDF {@link BNode}.
* @param tmp
* The buffer used to format the toKey (optional). A new
* byte[] will be allocated if this is null, but the
* same byte[] can be reused for multiple invocations. The buffer
* MUST be dimensioned to
* {@link BlobsIndexHelper#SIZEOF_PREFIX_KEY}.
*
* @return The collision counter.
*
* @throws CollisionBucketSizeException
* if an attempt is made to insert a {@link Value} into a
* collision bucket which is full.
*/
public int addBNode(final IIndex ndx, final IKeyBuilder keyBuilder,
final byte[] baseKey, final byte[] val, final byte[] tmp) {
/*
* The fromKey is strictly LT any full key for the hash code of this val
* but strictly GT any key have a hash code LT the hash code of this
* val.
*/
final byte[] fromKey = baseKey;
// key strictly LT any successor of the hash code of this val.
final byte[] toKey = makeToKey(fromKey, tmp);
// fast range count. this tells us how many collisions there are.
// this is an exact collision count since we are not deleting tuples
// from the TERMS index.
final long rangeCount = ndx.rangeCount(fromKey, toKey);
if (rangeCount >= MAX_COUNTER) {
/*
* Impose a hard limit on the #of hash collisions we will accept in
* this utility.
*/
throw new CollisionBucketSizeException(rangeCount);
}
// // Force range count into (signed) byte
// final byte counter = (byte) rangeCount;
// Form a key using the collision counter (guaranteed distinct).
final byte[] key = makeKey(keyBuilder.reset(), baseKey,
(int) rangeCount);
// Insert into the index.
if (ndx.insert(key, val) != null) {
throw new AssertionError();
}
if (rangeCount >= LOG_WARN_COUNTER_THRESHOLD) {
log.warn("Collision: hashCode=" + BytesUtil.toString(key)
+ ", collisionBucketSize=" + rangeCount);
}
return (int) rangeCount;
}
/**
* Return the value associated with the {@link BlobIV} in the TERMS index.
*
* Note: The returned byte[] may be decoded using the
* {@link BigdataValueSerializer} associated with the
* {@link BigdataValueFactory} for the namespace of the owning
* {@link AbstractTripleStore}.
*
* @param ndx
* The index.
* @param iv
* The {@link IV}.
* @param keyBuilder
* An object used to format the {@link IV} as a key for the
* index.
*
* @return The byte[] value -or- null if there is no entry for
* that {@link IV} in the index.
*/
public byte[] lookup(final IIndex ndx, final BlobIV iv,
final IKeyBuilder keyBuilder) {
final byte[] key = iv.encode(keyBuilder.reset()).getKey();
return ndx.lookup(key);
}
/**
* Create a fully formed key for the TERMS index from a baseKey and a hash
* collision counter.
*
* @param keyBuilder
* The caller is responsible for resetting the buffer as
* required.
* @param baseKey
* The base key (including the flags byte and the hashCode).
* @param counter
* The counter value.
*
* @return The fully formed key.
*/
public byte[] makeKey(final IKeyBuilder keyBuilder, final byte[] baseKey,
final int counter) {
final byte[] key = keyBuilder.append(baseKey).append((short) counter)
.getKey();
assert key.length == TERMS_INDEX_KEY_SIZE;
return key;
}
/**
* Create a fully formed key for the TERMS index from the {@link VTE}, the
* hashCode of the {@link BigdataValue}, and the hash collision counter.
*
* @param keyBuilder
* The caller is responsible for resetting the buffer as
* required.
* @param vte
* The {@link VTE}.
* @param hashCode
* The hash code of the {@link BigdataValue}.
* @param counter
* The hash collision counter.
*
* @return The fully formed key.
*/
// Note: Only used by the unit tests.
public byte[] makeKey(final IKeyBuilder keyBuilder, final VTE vte,
final int hashCode, final int counter) {
/*
* Note: This MUST agree with TermId#encode().
*/
keyBuilder.appendSigned(BlobIV.toFlags(vte)); // flags byte
keyBuilder.appendSigned(INonInlineExtensionCodes.BlobIV); // extension byte.
keyBuilder.append(hashCode); // hashCode
keyBuilder.append((short) counter); // hash collision counter.
final byte[] key = keyBuilder.getKey();
assert key.length == TERMS_INDEX_KEY_SIZE;
return key;
}
/**
* Create a prefix key for the TERMS index from the {@link VTE} and hashCode
* of the {@link BigdataValue}.
*
* @param keyBuilder
* The caller is responsible for resetting the buffer as
* required.
* @param vte
* The {@link VTE}.
* @param hashCode
* The hash code of the {@link BigdataValue}.
*
* @return The prefix key.
*/
public byte[] makePrefixKey(final IKeyBuilder keyBuilder, final VTE vte,
final int hashCode) {
/*
* Note: This MUST agree with TermId#encode().
*/
// flags byte
keyBuilder.appendSigned(BlobIV.toFlags(vte));
// extension byte.
keyBuilder.appendSigned(INonInlineExtensionCodes.BlobIV);
// hashCode
keyBuilder.append(hashCode);
final byte[] prefixKey = keyBuilder.getKey();
assert prefixKey.length == SIZEOF_PREFIX_KEY;
return prefixKey;
}
/**
* Create a prefix key for the TERMS index from the {@link BigdataValue}.
*
* @param keyBuilder
* The caller is responsible for resetting the buffer as
* required.
* @param value
* The {@link BigdataValue}
*
* @return The prefix key.
*/
public byte[] makePrefixKey(final IKeyBuilder keyBuilder,
final BigdataValue value) {
final VTE vte = VTE.valueOf(value);
return makePrefixKey(keyBuilder, vte, value.hashCode());
}
/**
* Generate the successor of the fromKey.
*
* @param fromKey
* The fromKey.
* @param tmp
* The buffer used to format the toKey (optional). A new
* byte[] will be allocated if this is null, but the
* same byte[] can be reused for multiple invocations. The buffer
* MUST be dimensioned to
* {@link BlobsIndexHelper#TERMS_INDEX_KEY_SIZE}.
*
* @return The toKey.
*/
byte[] makeToKey(final byte[] fromKey, final byte[] tmp) {
assert fromKey.length == SIZEOF_PREFIX_KEY;
final byte[] toKey;
if (tmp == null) {
// Allocate a temporary buffer.
toKey = new byte[SIZEOF_PREFIX_KEY];
} else if (tmp.length != SIZEOF_PREFIX_KEY) {
// Caller's buffer is the wrong size.
throw new IllegalArgumentException();
} else {
// Use the caller's buffer.
toKey = tmp;
}
// Copy the fromKey into the temporary buffer.
System.arraycopy(fromKey, 0/* srcPos */, toKey/* dest */, 0/* destPos */,
SIZEOF_PREFIX_KEY/* length */);
// Form the successor (side-effect on the toKey buffer).
SuccessorUtil.successor(toKey);
// Return the successor of the fromKey.
return tmp;
}
/**
* Return a new {@link IKeyBuilder} suitable for formatting keys for the
* TERMS index.
*
* @return The {@link IKeyBuilder}.
*/
public IKeyBuilder newKeyBuilder() {
return new KeyBuilder(TERMS_INDEX_KEY_SIZE);
}
/**
* Exception thrown if the maximum size of the collision bucket would be
* exceeded for some {@link BigdataValue}.
*
* @author thompsonbry
*/
public static class CollisionBucketSizeException extends RuntimeException {
/**
*
*/
private static final long serialVersionUID = 1L;
public CollisionBucketSizeException(final long rangeCount) {
super("ncoll=" + rangeCount);
}
}
}