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Sail implementation that stores data directly to disk in dedicated file formats.
/*******************************************************************************
* Copyright (c) 2015 Eclipse RDF4J contributors, Aduna, and others.
* 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.
*******************************************************************************/
package org.eclipse.rdf4j.sail.nativerdf;
import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
import java.util.Optional;
import org.eclipse.rdf4j.common.annotation.InternalUseOnly;
import org.eclipse.rdf4j.common.concurrent.locks.Lock;
import org.eclipse.rdf4j.common.concurrent.locks.ReadWriteLockManager;
import org.eclipse.rdf4j.common.concurrent.locks.WritePrefReadWriteLockManager;
import org.eclipse.rdf4j.common.io.ByteArrayUtil;
import org.eclipse.rdf4j.model.BNode;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Literal;
import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.util.Literals;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.model.vocabulary.XSD;
import org.eclipse.rdf4j.sail.SailException;
import org.eclipse.rdf4j.sail.nativerdf.datastore.DataStore;
import org.eclipse.rdf4j.sail.nativerdf.model.NativeBNode;
import org.eclipse.rdf4j.sail.nativerdf.model.NativeIRI;
import org.eclipse.rdf4j.sail.nativerdf.model.NativeLiteral;
import org.eclipse.rdf4j.sail.nativerdf.model.NativeResource;
import org.eclipse.rdf4j.sail.nativerdf.model.NativeValue;
/**
* File-based indexed storage and retrieval of RDF values. ValueStore maps RDF values to integer IDs and vice-versa.
*
* @author Arjohn Kampman
*
* @apiNote This feature is for internal use only: its existence, signature or behavior may change without warning from
* one release to the next.
*/
@InternalUseOnly
public class ValueStore extends SimpleValueFactory {
/*-----------*
* Constants *
*-----------*/
/**
* The default value cache size.
*/
public static final int VALUE_CACHE_SIZE = 512;
/**
* The default value id cache size.
*/
public static final int VALUE_ID_CACHE_SIZE = 128;
/**
* The default namespace cache size.
*/
public static final int NAMESPACE_CACHE_SIZE = 64;
/**
* The default namespace id cache size.
*/
public static final int NAMESPACE_ID_CACHE_SIZE = 32;
private static final String FILENAME_PREFIX = "values";
private static final byte URI_VALUE = 0x1; // 0000 0001
private static final byte BNODE_VALUE = 0x2; // 0000 0010
private static final byte LITERAL_VALUE = 0x3; // 0000 0011
/*-----------*
* Variables *
*-----------*/
/**
* Used to do the actual storage of values, once they're translated to byte arrays.
*/
private final DataStore dataStore;
/**
* Lock manager used to prevent the removal of values over multiple method calls. Note that values can still be
* added when read locks are active.
*/
private final ReadWriteLockManager lockManager = new WritePrefReadWriteLockManager();
/**
* An object that indicates the revision of the value store, which is used to check if cached value IDs are still
* valid. In order to be valid, the ValueStoreRevision object of a NativeValue needs to be equal to this object.
*/
private volatile ValueStoreRevision revision;
/**
* A simple cache containing the [VALUE_CACHE_SIZE] most-recently used values stored by their ID.
*/
private final ConcurrentCache valueCache;
/**
* A simple cache containing the [ID_CACHE_SIZE] most-recently used value-IDs stored by their value.
*/
private final ConcurrentCache valueIDCache;
/**
* A simple cache containing the [NAMESPACE_CACHE_SIZE] most-recently used namespaces stored by their ID.
*/
private final ConcurrentCache namespaceCache;
/**
* A simple cache containing the [NAMESPACE_ID_CACHE_SIZE] most-recently used namespace-IDs stored by their
* namespace.
*/
private final ConcurrentCache namespaceIDCache;
/*--------------*
* Constructors *
*--------------*/
public ValueStore(File dataDir) throws IOException {
this(dataDir, false);
}
public ValueStore(File dataDir, boolean forceSync) throws IOException {
this(dataDir, forceSync, VALUE_CACHE_SIZE, VALUE_ID_CACHE_SIZE, NAMESPACE_CACHE_SIZE, NAMESPACE_ID_CACHE_SIZE);
}
public ValueStore(File dataDir, boolean forceSync, int valueCacheSize, int valueIDCacheSize, int namespaceCacheSize,
int namespaceIDCacheSize) throws IOException {
super();
dataStore = new DataStore(dataDir, FILENAME_PREFIX, forceSync);
valueCache = new ConcurrentCache<>(valueCacheSize);
valueIDCache = new ConcurrentCache<>(valueIDCacheSize);
namespaceCache = new ConcurrentCache<>(namespaceCacheSize);
namespaceIDCache = new ConcurrentCache<>(namespaceIDCacheSize);
setNewRevision();
}
/*---------*
* Methods *
*---------*/
/**
* Creates a new revision object for this value store, invalidating any IDs cached in NativeValue objects that were
* created by this value store.
*/
private void setNewRevision() {
revision = new ValueStoreRevision(this);
}
public ValueStoreRevision getRevision() {
return revision;
}
/**
* Gets a read lock on this value store that can be used to prevent values from being removed while the lock is
* active.
*/
public Lock getReadLock() throws InterruptedException {
return lockManager.getReadLock();
}
/**
* Gets the value for the specified ID.
*
* @param id A value ID.
* @return The value for the ID, or null no such value could be found.
* @exception IOException If an I/O error occurred.
*/
public NativeValue getValue(int id) throws IOException {
// Check value cache
Integer cacheID = id;
NativeValue resultValue = valueCache.get(cacheID);
if (resultValue == null) {
// Value not in cache, fetch it from file
byte[] data = dataStore.getData(id);
if (data != null) {
resultValue = data2value(id, data);
// Store value in cache
valueCache.put(cacheID, resultValue);
}
}
return resultValue;
}
/**
* Gets the ID for the specified value.
*
* @param value A value.
* @return The ID for the specified value, or {@link NativeValue#UNKNOWN_ID} if no such ID could be found.
* @exception IOException If an I/O error occurred.
*/
public int getID(Value value) throws IOException {
// Try to get the internal ID from the value itself
boolean isOwnValue = isOwnValue(value);
if (isOwnValue) {
NativeValue nativeValue = (NativeValue) value;
if (revisionIsCurrent(nativeValue)) {
int id = nativeValue.getInternalID();
if (id != NativeValue.UNKNOWN_ID) {
return id;
}
}
}
// Check cache
Integer cachedID = valueIDCache.get(value);
if (cachedID != null) {
int id = cachedID.intValue();
if (isOwnValue) {
// Store id in value for fast access in any consecutive calls
((NativeValue) value).setInternalID(id, revision);
}
return id;
}
// ID not cached, search in file
byte[] data = value2data(value, false);
if (data == null && value instanceof Literal) {
data = literal2legacy((Literal) value);
}
if (data != null) {
int id = dataStore.getID(data);
if (id == NativeValue.UNKNOWN_ID && value instanceof Literal) {
id = dataStore.getID(literal2legacy((Literal) value));
}
if (id != NativeValue.UNKNOWN_ID) {
if (isOwnValue) {
// Store id in value for fast access in any consecutive calls
((NativeValue) value).setInternalID(id, revision);
} else {
// Store id in cache
NativeValue nv = getNativeValue(value);
nv.setInternalID(id, revision);
valueIDCache.put(nv, Integer.valueOf(id));
}
}
return id;
}
return NativeValue.UNKNOWN_ID;
}
/**
* Stores the supplied value and returns the ID that has been assigned to it. In case the value was already present,
* the value will not be stored again and the ID of the existing value is returned.
*
* @param value The Value to store.
* @return The ID that has been assigned to the value.
* @exception IOException If an I/O error occurred.
*/
public int storeValue(Value value) throws IOException {
// Try to get the internal ID from the value itself
boolean isOwnValue = isOwnValue(value);
if (isOwnValue) {
NativeValue nativeValue = (NativeValue) value;
if (revisionIsCurrent(nativeValue)) {
// Value's ID is still current
int id = nativeValue.getInternalID();
if (id != NativeValue.UNKNOWN_ID) {
return id;
}
}
}
// ID not stored in value itself, try the ID cache
Integer cachedID = valueIDCache.get(value);
if (cachedID != null) {
int id = cachedID.intValue();
if (isOwnValue) {
// Store id in value for fast access in any consecutive calls
((NativeValue) value).setInternalID(id, revision);
}
return id;
}
// Unable to get internal ID in a cheap way, just store it in the data
// store which will handle duplicates
byte[] valueData = value2data(value, true);
int id = dataStore.storeData(valueData);
NativeValue nv = isOwnValue ? (NativeValue) value : getNativeValue(value);
// Store id in value for fast access in any consecutive calls
nv.setInternalID(id, revision);
// Update cache
valueIDCache.put(nv, id);
return id;
}
/**
* Removes all values from the ValueStore.
*
* @exception IOException If an I/O error occurred.
*/
public void clear() throws IOException {
try {
Lock writeLock = lockManager.getWriteLock();
try {
dataStore.clear();
valueCache.clear();
valueIDCache.clear();
namespaceCache.clear();
namespaceIDCache.clear();
setNewRevision();
} finally {
writeLock.release();
}
} catch (InterruptedException e) {
throw new IOException("Failed to acquire write lock", e);
}
}
/**
* Synchronizes any changes that are cached in memory to disk.
*
* @exception IOException If an I/O error occurred.
*/
public void sync() throws IOException {
dataStore.sync();
}
/**
* Closes the ValueStore, releasing any file references, etc. Once closed, the ValueStore can no longer be used.
*
* @exception IOException If an I/O error occurred.
*/
public void close() throws IOException {
dataStore.close();
}
/**
* Checks that every value has exactly one ID.
*
* @throws IOException
*/
public void checkConsistency() throws SailException, IOException {
int maxID = dataStore.getMaxID();
for (int id = 1; id <= maxID; id++) {
byte[] data = dataStore.getData(id);
if (isNamespaceData(data)) {
String namespace = data2namespace(data);
try {
if (id == getNamespaceID(namespace, false)
&& java.net.URI.create(namespace + "part").isAbsolute()) {
continue;
}
} catch (IllegalArgumentException e) {
// throw SailException
}
throw new SailException(
"Store must be manually exported and imported to fix namespaces like " + namespace);
} else {
Value value = this.data2value(id, data);
if (id != this.getID(copy(value))) {
throw new SailException(
"Store must be manually exported and imported to merge values like " + value);
}
}
}
}
private Value copy(Value value) {
if (value instanceof IRI) {
return createIRI(value.stringValue());
} else if (value instanceof Literal) {
Literal lit = (Literal) value;
if (Literals.isLanguageLiteral(lit)) {
return createLiteral(value.stringValue(), lit.getLanguage().orElse(null));
} else {
return createLiteral(value.stringValue(), lit.getDatatype());
}
} else {
return createBNode(value.stringValue());
}
}
/**
* Checks if the supplied Value object is a NativeValue object that has been created by this ValueStore.
*/
private boolean isOwnValue(Value value) {
return value instanceof NativeValue && ((NativeValue) value).getValueStoreRevision().getValueStore() == this;
}
/**
* Checks if the revision of the supplied value object is still current.
*/
private boolean revisionIsCurrent(NativeValue value) {
return revision.equals(value.getValueStoreRevision());
}
private byte[] value2data(Value value, boolean create) throws IOException {
if (value instanceof IRI) {
return uri2data((IRI) value, create);
} else if (value instanceof BNode) {
return bnode2data((BNode) value, create);
} else if (value instanceof Literal) {
return literal2data((Literal) value, create);
} else {
throw new IllegalArgumentException("value parameter should be a URI, BNode or Literal");
}
}
private byte[] uri2data(IRI uri, boolean create) throws IOException {
int nsID = getNamespaceID(uri.getNamespace(), create);
if (nsID == -1) {
// Unknown namespace means unknown URI
return null;
}
// Get local name in UTF-8
byte[] localNameData = uri.getLocalName().getBytes(StandardCharsets.UTF_8);
// Combine parts in a single byte array
byte[] uriData = new byte[5 + localNameData.length];
uriData[0] = URI_VALUE;
ByteArrayUtil.putInt(nsID, uriData, 1);
ByteArrayUtil.put(localNameData, uriData, 5);
return uriData;
}
private byte[] bnode2data(BNode bNode, boolean create) throws IOException {
byte[] idData = bNode.getID().getBytes(StandardCharsets.UTF_8);
byte[] bNodeData = new byte[1 + idData.length];
bNodeData[0] = BNODE_VALUE;
ByteArrayUtil.put(idData, bNodeData, 1);
return bNodeData;
}
private byte[] literal2data(Literal literal, boolean create) throws IOException {
return literal2data(literal.getLabel(), literal.getLanguage(), literal.getDatatype(), create);
}
private byte[] literal2legacy(Literal literal) throws IOException {
IRI dt = literal.getDatatype();
if (XSD.STRING.equals(dt) || RDF.LANGSTRING.equals(dt)) {
return literal2data(literal.getLabel(), literal.getLanguage(), null, false);
}
return literal2data(literal.getLabel(), literal.getLanguage(), dt, false);
}
private byte[] literal2data(String label, Optional lang, IRI dt, boolean create)
throws IOException, UnsupportedEncodingException {
// Get datatype ID
int datatypeID = NativeValue.UNKNOWN_ID;
if (create) {
datatypeID = storeValue(dt);
} else if (dt != null) {
datatypeID = getID(dt);
if (datatypeID == NativeValue.UNKNOWN_ID) {
// Unknown datatype means unknown literal
return null;
}
}
// Get language tag in UTF-8
byte[] langData = null;
int langDataLength = 0;
if (lang.isPresent()) {
langData = lang.get().getBytes(StandardCharsets.UTF_8);
langDataLength = langData.length;
}
// Get label in UTF-8
byte[] labelData = label.getBytes(StandardCharsets.UTF_8);
// Combine parts in a single byte array
byte[] literalData = new byte[6 + langDataLength + labelData.length];
literalData[0] = LITERAL_VALUE;
ByteArrayUtil.putInt(datatypeID, literalData, 1);
literalData[5] = (byte) langDataLength;
if (langData != null) {
ByteArrayUtil.put(langData, literalData, 6);
}
ByteArrayUtil.put(labelData, literalData, 6 + langDataLength);
return literalData;
}
private boolean isNamespaceData(byte[] data) {
return data[0] != URI_VALUE && data[0] != BNODE_VALUE && data[0] != LITERAL_VALUE;
}
private NativeValue data2value(int id, byte[] data) throws IOException {
switch (data[0]) {
case URI_VALUE:
return data2uri(id, data);
case BNODE_VALUE:
return data2bnode(id, data);
case LITERAL_VALUE:
return data2literal(id, data);
default:
throw new IllegalArgumentException("Namespaces cannot be converted into values: " + data2namespace(data));
}
}
private NativeIRI data2uri(int id, byte[] data) throws IOException {
int nsID = ByteArrayUtil.getInt(data, 1);
String namespace = getNamespace(nsID);
String localName = new String(data, 5, data.length - 5, StandardCharsets.UTF_8);
return new NativeIRI(revision, namespace, localName, id);
}
private NativeBNode data2bnode(int id, byte[] data) throws IOException {
String nodeID = new String(data, 1, data.length - 1, StandardCharsets.UTF_8);
return new NativeBNode(revision, nodeID, id);
}
private NativeLiteral data2literal(int id, byte[] data) throws IOException {
// Get datatype
int datatypeID = ByteArrayUtil.getInt(data, 1);
IRI datatype = null;
if (datatypeID != NativeValue.UNKNOWN_ID) {
datatype = (IRI) getValue(datatypeID);
}
// Get language tag
String lang = null;
int langLength = data[5];
if (langLength > 0) {
lang = new String(data, 6, langLength, StandardCharsets.UTF_8);
}
// Get label
String label = new String(data, 6 + langLength, data.length - 6 - langLength, StandardCharsets.UTF_8);
if (lang != null) {
return new NativeLiteral(revision, label, lang, id);
} else if (datatype != null) {
return new NativeLiteral(revision, label, datatype, id);
} else {
return new NativeLiteral(revision, label, XSD.STRING, id);
}
}
private String data2namespace(byte[] data) throws UnsupportedEncodingException {
return new String(data, StandardCharsets.UTF_8);
}
private int getNamespaceID(String namespace, boolean create) throws IOException {
Integer cacheID = namespaceIDCache.get(namespace);
if (cacheID != null) {
return cacheID;
}
byte[] namespaceData = namespace.getBytes(StandardCharsets.UTF_8);
int id;
if (create) {
id = dataStore.storeData(namespaceData);
} else {
id = dataStore.getID(namespaceData);
}
if (id != -1) {
namespaceIDCache.put(namespace, id);
}
return id;
}
private String getNamespace(int id) throws IOException {
Integer cacheID = id;
String namespace = namespaceCache.get(cacheID);
if (namespace == null) {
byte[] namespaceData = dataStore.getData(id);
namespace = data2namespace(namespaceData);
namespaceCache.put(cacheID, namespace);
}
return namespace;
}
/*-------------------------------------*
* Methods from interface ValueFactory *
*-------------------------------------*/
@Override
public NativeIRI createIRI(String uri) {
return new NativeIRI(revision, uri);
}
@Override
public NativeIRI createIRI(String namespace, String localName) {
return new NativeIRI(revision, namespace, localName);
}
@Override
public NativeBNode createBNode(String nodeID) {
return new NativeBNode(revision, nodeID);
}
@Override
public NativeLiteral createLiteral(String value) {
return new NativeLiteral(revision, value, XSD.STRING);
}
@Override
public NativeLiteral createLiteral(String value, String language) {
return new NativeLiteral(revision, value, language);
}
@Override
public NativeLiteral createLiteral(String value, IRI datatype) {
return new NativeLiteral(revision, value, datatype);
}
/*----------------------------------------------------------------------*
* Methods for converting model objects to NativeStore-specific objects *
*----------------------------------------------------------------------*/
public NativeValue getNativeValue(Value value) {
if (value instanceof Resource) {
return getNativeResource((Resource) value);
} else if (value instanceof Literal) {
return getNativeLiteral((Literal) value);
} else {
throw new IllegalArgumentException("Unknown value type: " + value.getClass());
}
}
public NativeResource getNativeResource(Resource resource) {
if (resource instanceof IRI) {
return getNativeURI((IRI) resource);
} else if (resource instanceof BNode) {
return getNativeBNode((BNode) resource);
} else {
throw new IllegalArgumentException("Unknown resource type: " + resource.getClass());
}
}
/**
* Creates a NativeURI that is equal to the supplied URI. This method returns the supplied URI itself if it is
* already a NativeURI that has been created by this ValueStore, which prevents unnecessary object creations.
*
* @return A NativeURI for the specified URI.
*/
public NativeIRI getNativeURI(IRI uri) {
if (isOwnValue(uri)) {
return (NativeIRI) uri;
}
return new NativeIRI(revision, uri.toString());
}
/**
* Creates a NativeBNode that is equal to the supplied bnode. This method returns the supplied bnode itself if it is
* already a NativeBNode that has been created by this ValueStore, which prevents unnecessary object creations.
*
* @return A NativeBNode for the specified bnode.
*/
public NativeBNode getNativeBNode(BNode bnode) {
if (isOwnValue(bnode)) {
return (NativeBNode) bnode;
}
return new NativeBNode(revision, bnode.getID());
}
/**
* Creates an NativeLiteral that is equal to the supplied literal. This method returns the supplied literal itself
* if it is already a NativeLiteral that has been created by this ValueStore, which prevents unnecessary object
* creations.
*
* @return A NativeLiteral for the specified literal.
*/
public NativeLiteral getNativeLiteral(Literal l) {
if (isOwnValue(l)) {
return (NativeLiteral) l;
}
if (Literals.isLanguageLiteral(l)) {
return new NativeLiteral(revision, l.getLabel(), l.getLanguage().get());
} else {
NativeIRI datatype = getNativeURI(l.getDatatype());
return new NativeLiteral(revision, l.getLabel(), datatype);
}
}
/*--------------------*
* Test/debug methods *
*--------------------*/
public static void main(String[] args) throws Exception {
File dataDir = new File(args[0]);
ValueStore valueStore = new ValueStore(dataDir);
int maxID = valueStore.dataStore.getMaxID();
for (int id = 1; id <= maxID; id++) {
byte[] data = valueStore.dataStore.getData(id);
if (valueStore.isNamespaceData(data)) {
String ns = valueStore.data2namespace(data);
System.out.println("[" + id + "] " + ns);
} else {
Value value = valueStore.data2value(id, data);
System.out.println("[" + id + "] " + value.toString());
}
}
}
}
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