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The Archive Commons Code Libraries project contains general Java utility
libraries, as used by the Heritrix crawler and other projects.
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/*
* This file is part of the Heritrix web crawler (crawler.archive.org).
*
* Licensed to the Internet Archive (IA) by one or more individual
* contributors.
*
* The IA licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.archive.bdb;
import java.io.Closeable;
import java.io.File;
import java.io.FileFilter;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.math.BigInteger;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.filefilter.FileFilterUtils;
import org.apache.commons.io.filefilter.IOFileFilter;
import org.archive.checkpointing.Checkpoint;
import org.archive.checkpointing.Checkpointable;
import org.archive.spring.ConfigPath;
import org.archive.util.IdentityCacheable;
import org.archive.util.ObjectIdentityBdbManualCache;
import org.archive.util.ObjectIdentityCache;
import org.archive.util.TextUtils;
import org.archive.util.bdbje.EnhancedEnvironment;
import org.springframework.beans.factory.DisposableBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.Lifecycle;
import com.sleepycat.bind.EntryBinding;
import com.sleepycat.bind.serial.SerialBinding;
import com.sleepycat.bind.serial.StoredClassCatalog;
import com.sleepycat.bind.tuple.TupleBinding;
import com.sleepycat.je.CheckpointConfig;
import com.sleepycat.je.Database;
import com.sleepycat.je.DatabaseConfig;
import com.sleepycat.je.DatabaseException;
import com.sleepycat.je.DatabaseNotFoundException;
import com.sleepycat.je.EnvironmentConfig;
import com.sleepycat.je.util.DbBackup;
/**
* Utility module for managing a shared BerkeleyDB-JE environment
*
* @author pjack
* @author gojomo
*/
public class BdbModule implements Lifecycle, Checkpointable, Closeable, DisposableBean {
final private static Logger LOGGER =
Logger.getLogger(BdbModule.class.getName());
private static class DatabasePlusConfig implements Serializable {
private static final long serialVersionUID = 1L;
public transient Database database;
public BdbConfig config;
}
/**
* Configuration object for databases. Needed because
* {@link DatabaseConfig} is not serializable. Also it prevents invalid
* configurations. (All databases opened through this module must be
* deferred-write, because otherwise they can't sync(), and you can't
* run a checkpoint without doing sync() first.)
*
* @author pjack
*
*/
public static class BdbConfig implements Serializable {
private static final long serialVersionUID = 1L;
protected boolean allowCreate;
protected boolean sortedDuplicates;
protected boolean transactional;
protected boolean deferredWrite = true;
public BdbConfig() {
}
public boolean isAllowCreate() {
return allowCreate;
}
public void setAllowCreate(boolean allowCreate) {
this.allowCreate = allowCreate;
}
public boolean getSortedDuplicates() {
return sortedDuplicates;
}
public void setSortedDuplicates(boolean sortedDuplicates) {
this.sortedDuplicates = sortedDuplicates;
}
public DatabaseConfig toDatabaseConfig() {
DatabaseConfig result = new DatabaseConfig();
result.setDeferredWrite(deferredWrite);
result.setTransactional(transactional);
result.setAllowCreate(allowCreate);
result.setSortedDuplicates(sortedDuplicates);
return result;
}
public boolean isTransactional() {
return transactional;
}
public void setTransactional(boolean transactional) {
this.transactional = transactional;
}
public void setDeferredWrite(boolean b) {
this.deferredWrite = true;
}
}
protected ConfigPath dir = new ConfigPath("bdbmodule subdirectory","state");
public ConfigPath getDir() {
return dir;
}
public void setDir(ConfigPath dir) {
this.dir = dir;
}
protected int cachePercent = -1;
public int getCachePercent() {
return cachePercent;
}
public void setCachePercent(int cachePercent) {
this.cachePercent = cachePercent;
}
protected int cacheSize = -1;
public int getCacheSize() {
return cacheSize;
}
public void setCacheSize(int cacheSize) {
this.cacheSize = cacheSize;
}
protected boolean useSharedCache = true;
public boolean getUseSharedCache() {
return useSharedCache;
}
public void setUseSharedCache(boolean useSharedCache) {
this.useSharedCache = useSharedCache;
}
protected long maxLogFileSize = 10000000;
public long getMaxLogFileSize() {
return maxLogFileSize;
}
public void setMaxLogFileSize(long maxLogFileSize) {
this.maxLogFileSize = maxLogFileSize;
}
/**
* Expected number of concurrent threads; used to tune nLockTables
* according to JE FAQ
* http://www.oracle.com/technology/products/berkeley-db/faq/je_faq.html#33
*/
protected int expectedConcurrency = 64;
public int getExpectedConcurrency() {
return expectedConcurrency;
}
public void setExpectedConcurrency(int expectedConcurrency) {
this.expectedConcurrency = expectedConcurrency;
}
/**
* Configure the number of cleaner threads (-1 means use the default)
* https://docs.oracle.com/cd/E17277_02/html/java/com/sleepycat/je/EnvironmentConfig.html#CLEANER_THREADS
*/
protected int jeCleanerThreads = -1;
public int getCleanerThreads() {
return jeCleanerThreads;
}
public void setCleanerThreads(int jeCleanerThreads) {
this.jeCleanerThreads = jeCleanerThreads;
}
/**
* Configure the number of evictor threads (-1 means use the default)
* https://docs.oracle.com/cd/E17277_02/html/java/com/sleepycat/je/EnvironmentConfig.html#EVICTOR_CORE_THREADS
*/
protected int evictorCoreThreads = -1;
public int getEvictorCoreThreads() {
return evictorCoreThreads;
}
public void setEvictorCoreThreads(int evictorCoreThreads) {
this.evictorCoreThreads = evictorCoreThreads;
}
/**
* Configure the maximum number of evictor threads (-1 means use the default)
* https://docs.oracle.com/cd/E17277_02/html/java/com/sleepycat/je/EnvironmentConfig.html#EVICTOR_MAX_THREADS
*/
protected int evictorMaxThreads = -1;
public int getEvictorMaxThreads() {
return evictorMaxThreads;
}
public void setEvictorMaxThreads(int evictorMaxThreads) {
this.evictorMaxThreads = evictorMaxThreads;
}
/**
* Whether to use hard-links to log files to collect/retain
* the BDB log files needed for a checkpoint. Default is true.
* May not work on Windows (especially on pre-NTFS filesystems).
* If false, the BDB 'je.cleaner.expunge' value will be set to
* 'false', as well, meaning BDB will *not* delete obsolete JDB
* files, but only rename the '.DEL'. They will have to be
* manually deleted to free disk space, but .DEL files referenced
* in any checkpoint's 'jdbfiles.manifest' should be retained to
* keep the checkpoint valid.
*/
protected boolean useHardLinkCheckpoints = true;
public boolean getUseHardLinkCheckpoints() {
return useHardLinkCheckpoints;
}
public void setUseHardLinkCheckpoints(boolean useHardLinkCheckpoints) {
this.useHardLinkCheckpoints = useHardLinkCheckpoints;
}
private transient EnhancedEnvironment bdbEnvironment;
private transient StoredClassCatalog classCatalog;
@SuppressWarnings("rawtypes")
private Map oiCaches =
new ConcurrentHashMap();
private Map databases =
new ConcurrentHashMap();
protected boolean isRunning = false;
public BdbModule() {
}
public synchronized void start() {
if (isRunning()) {
return;
}
isRunning = true;
try {
boolean isRecovery = false;
if(recoveryCheckpoint!=null) {
isRecovery = true;
doRecover();
}
setup(getDir().getFile(), !isRecovery);
} catch (DatabaseException e) {
throw new IllegalStateException(e);
} catch (IOException e) {
throw new IllegalStateException(e);
}
}
public boolean isRunning() {
return isRunning;
}
public void stop() {
isRunning = false;
}
protected void setup(File f, boolean create)
throws DatabaseException, IOException {
EnvironmentConfig config = new EnvironmentConfig();
config.setAllowCreate(create);
config.setLockTimeout(75, TimeUnit.MINUTES); // set to max
if (getCacheSize() > 0) {
config.setCacheSize(getCacheSize());
if (getCachePercent() > 0) {
LOGGER.warning("cachePercent and cacheSize are both set. Only cacheSize will be used.");
}
} else if (getCachePercent() > 0) {
config.setCachePercent(getCachePercent());
}
config.setSharedCache(getUseSharedCache());
// we take the advice literally from...
// https://web.archive.org/web/20100727081707/http://www.oracle.com/technology/products/berkeley-db/faq/je_faq.html#33
long nLockTables = getExpectedConcurrency()-1;
while(!BigInteger.valueOf(nLockTables).isProbablePrime(Integer.MAX_VALUE)) {
nLockTables--;
}
config.setConfigParam("je.lock.nLockTables", Long.toString(nLockTables));
// configure the number of cleaner threads, to speed up clearing out old state files:
int cleaners = getCleanerThreads();
if (cleaners > 0) {
config.setConfigParam(EnvironmentConfig.CLEANER_THREADS, Integer.toString(cleaners));
}
// configure number if evictor threads, to avoid critical eviction slowdowns:
int evictors = this.getEvictorCoreThreads();
if (evictors > -1) {
config.setConfigParam(EnvironmentConfig.EVICTOR_CORE_THREADS, Integer.toString(evictors));
}
int maxEvictors = this.getEvictorMaxThreads();
if (maxEvictors > 0) {
config.setConfigParam(EnvironmentConfig.EVICTOR_MAX_THREADS, Integer.toString(maxEvictors));
}
// triple this value to 6K because stats show many faults
config.setConfigParam("je.log.faultReadSize", "6144");
// set max bdb log file size. default 10M
config.setConfigParam("je.log.fileMax", Long.toString(getMaxLogFileSize()));
if(!getUseHardLinkCheckpoints()) {
// to support checkpoints by textual manifest only,
// prevent BDB's cleaner from deleting log files
config.setConfigParam("je.cleaner.expunge", "false");
} // else leave whatever other setting was already in place
org.archive.util.FileUtils.ensureWriteableDirectory(f);
this.bdbEnvironment = new EnhancedEnvironment(f, config);
this.classCatalog = this.bdbEnvironment.getClassCatalog();
if(!create) {
// freeze last log file -- so that originating checkpoint isn't fouled
DbBackup dbBackup = new DbBackup(bdbEnvironment);
dbBackup.startBackup();
dbBackup.endBackup();
}
}
public void closeDatabase(Database db) {
try {
closeDatabase(db.getDatabaseName());
} catch (DatabaseException e) {
LOGGER.log(Level.SEVERE, "Error getting db name", e);
}
}
public void closeDatabase(String name) {
DatabasePlusConfig dpc = databases.remove(name);
if (dpc == null) {
LOGGER.warning("No such database: " + name);
return;
}
Database db = dpc.database;
try {
db.sync();
} catch (DatabaseException e) {
LOGGER.log(Level.WARNING, "Error syncing when closing db " + name, e);
}
try {
db.close();
} catch (DatabaseException e) {
LOGGER.log(Level.WARNING, "Error closing db " + name, e);
}
}
/**
* Open a Database inside this BdbModule's environment, and
* remember it for automatic close-at-module-stop.
*
* @param name
* @param config
* @param usePriorData
* @throws DatabaseException
*/
public Database openDatabase(String name, BdbConfig config, boolean usePriorData)
throws DatabaseException {
if (bdbEnvironment == null) {
// proper initialization hasn't occurred
throw new IllegalStateException("BdbModule not started");
}
if (databases.containsKey(name)) {
DatabasePlusConfig dpc = databases.get(name);
if(dpc.config == config) {
// object-identical configs: OK to share DB
return dpc.database;
}
// unshared config object: might be name collision; error
throw new IllegalStateException("Database already exists: " +name);
}
DatabasePlusConfig dpc = new DatabasePlusConfig();
if (!usePriorData) {
try {
bdbEnvironment.truncateDatabase(null, name, false);
} catch (DatabaseNotFoundException e) {
// Ignored
}
}
dpc.database = bdbEnvironment.openDatabase(null, name, config.toDatabaseConfig());
dpc.config = config;
databases.put(name, dpc);
return dpc.database;
}
public StoredClassCatalog getClassCatalog() {
return classCatalog;
}
public StoredQueue getStoredQueue(String dbname, Class clazz, boolean usePriorData) {
try {
Database queueDb;
queueDb = openDatabase(dbname,
StoredQueue.databaseConfig(), usePriorData);
return new StoredQueue(queueDb, clazz, getClassCatalog());
} catch (DatabaseException e) {
throw new RuntimeException(e);
}
}
/**
* Get an ObjectIdentityBdbCache, backed by a BDB Database of the
* given name, with the given value class type. If 'recycle' is true,
* reuse values already in the database; otherwise start with an
* empty cache.
*
* @param
* @param dbName
* @param recycle
* @param valueClass
* @throws DatabaseException
*/
public ObjectIdentityBdbManualCache getOIBCCache(String dbName, boolean recycle,
Class valueClass)
throws DatabaseException {
if (!recycle) {
try {
bdbEnvironment.truncateDatabase(null, dbName, false);
} catch (DatabaseNotFoundException e) {
// ignored
}
}
ObjectIdentityBdbManualCache oic = new ObjectIdentityBdbManualCache();
oic.initialize(bdbEnvironment, dbName, valueClass, classCatalog);
oiCaches.put(dbName, oic);
return oic;
}
public ObjectIdentityCache getObjectCache(String dbName, boolean recycle,
Class valueClass)
throws DatabaseException {
return getObjectCache(dbName, recycle, valueClass, valueClass);
}
/**
* Get an ObjectIdentityCache, backed by a BDB Database of the given
* name, with objects of the given valueClass type. If 'recycle' is
* true, reuse values already in the database; otherwise start with
* an empty cache.
*
* @param
* @param dbName
* @param recycle
* @param valueClass
* @throws DatabaseException
*/
public ObjectIdentityCache getObjectCache(String dbName, boolean recycle,
Class declaredClass, Class valueClass)
throws DatabaseException {
@SuppressWarnings("unchecked")
ObjectIdentityCache oic = oiCaches.get(dbName);
if(oic!=null) {
return oic;
}
oic = getOIBCCache(dbName, recycle, valueClass);
return oic;
}
private void writeObject(ObjectOutputStream out) throws IOException {
out.defaultWriteObject();
}
public void startCheckpoint(Checkpoint checkpointInProgress) {}
public void doCheckpoint(final Checkpoint checkpointInProgress) throws IOException {
// First sync objectCaches
for (@SuppressWarnings("rawtypes") ObjectIdentityCache oic : oiCaches.values()) {
oic.sync();
}
try {
// sync all databases
for (DatabasePlusConfig dbc: databases.values()) {
dbc.database.sync();
}
// Do a force checkpoint. That's what a sync does (i.e. doSync).
CheckpointConfig chkptConfig = new CheckpointConfig();
chkptConfig.setForce(true);
// Mark Hayes of sleepycat says:
// "The default for this property is false, which gives the current
// behavior (allow deltas). If this property is true, deltas are
// prohibited -- full versions of internal nodes are always logged
// during the checkpoint. When a full version of an internal node
// is logged during a checkpoint, recovery does not need to process
// it at all. It is only fetched if needed by the application,
// during normal DB operations after recovery. When a delta of an
// internal node is logged during a checkpoint, recovery must
// process it by fetching the full version of the node from earlier
// in the log, and then applying the delta to it. This can be
// pretty slow, since it is potentially a large amount of
// random I/O."
// chkptConfig.setMinimizeRecoveryTime(true);
bdbEnvironment.checkpoint(chkptConfig);
LOGGER.fine("Finished bdb checkpoint.");
DbBackup dbBackup = new DbBackup(bdbEnvironment);
try {
dbBackup.startBackup();
File envCpDir = new File(dir.getFile(),checkpointInProgress.getName());
org.archive.util.FileUtils.ensureWriteableDirectory(envCpDir);
File logfilesList = new File(envCpDir,"jdbfiles.manifest");
String[] filedata = dbBackup.getLogFilesInBackupSet();
for (int i=0; i filesAndLengths = FileUtils.readLines(logfilesList);
HashMap retainLogfiles = new HashMap();
for(String line : filesAndLengths) {
String[] fileAndLength = line.split(",");
long expectedLength = Long.valueOf(fileAndLength[1]);
retainLogfiles.put(fileAndLength[0],expectedLength);
// check for files in checkpoint directory; relink to environment as necessary
File cpFile = new File(cpDir, line);
File destFile = new File(dir.getFile(), fileAndLength[0]);
if(cpFile.exists()) {
if(cpFile.length()!=expectedLength) {
LOGGER.warning(cpFile.getName()+" expected "+expectedLength+" actual "+cpFile.length());
// TODO: is truncation necessary?
}
if(destFile.exists()) {
if(!destFile.delete()) {
LOGGER.log(Level.SEVERE, "unable to delete obstructing file "+destFile);
}
}
try {
Files.createLink(destFile.toPath(), cpFile.toPath().toAbsolutePath());
} catch (IOException | UnsupportedOperationException e) {
LOGGER.log(Level.SEVERE, "unable to create required restore link " + destFile, e);
}
}
}
IOFileFilter filter = FileFilterUtils.orFileFilter(
FileFilterUtils.suffixFileFilter(".jdb"),
FileFilterUtils.suffixFileFilter(".del"));
filter = FileFilterUtils.makeFileOnly(filter);
// reverify environment directory is as it was at checkpoint time,
// deleting any extra files
for(File f : dir.getFile().listFiles((FileFilter)filter)) {
if(retainLogfiles.containsKey(f.getName())) {
// named file still exists under original name
long expectedLength = retainLogfiles.get(f.getName());
if(f.length()!=expectedLength) {
LOGGER.warning(f.getName()+" expected "+expectedLength+" actual "+f.length());
// TODO: truncate? this unexpected length mismatch
// probably only happens if there was already a recovery
// where the affected file was the last of the set, in
// which case BDB appends a small amount of (harmless?) data
// to the previously-undersized file
}
retainLogfiles.remove(f.getName());
continue;
}
// file as now-named not in restore set; check if un-".DEL" renaming needed
String undelName = f.getName().replace(".del", ".jdb");
if(retainLogfiles.containsKey(undelName)) {
// file if renamed matches desired file name
long expectedLength = retainLogfiles.get(undelName);
if(f.length()!=expectedLength) {
LOGGER.warning(f.getName()+" expected "+expectedLength+" actual "+f.length());
// TODO: truncate to expected size?
}
if(!f.renameTo(new File(f.getParentFile(),undelName))) {
throw new IOException("Unable to rename " + f + " to " +
undelName);
}
retainLogfiles.remove(undelName);
}
// file not needed; delete/move-aside
if(!f.delete()) {
LOGGER.warning("unable to delete "+f);
org.archive.util.FileUtils.moveAsideIfExists(f);
}
// TODO: log/warn of ruined later checkpoints?
}
if(retainLogfiles.size()>0) {
// some needed files weren't present
LOGGER.severe("Checkpoint corrupt, needed log files missing: "+retainLogfiles);
}
}
public void finishCheckpoint(Checkpoint checkpointInProgress) {}
protected Checkpoint recoveryCheckpoint;
@Autowired(required=false)
public void setRecoveryCheckpoint(Checkpoint checkpoint) {
this.recoveryCheckpoint = checkpoint;
}
public void close() {
if (classCatalog == null) {
return;
}
for(@SuppressWarnings("rawtypes") ObjectIdentityCache cache : oiCaches.values()) {
try {
cache.close();
} catch (Exception e) {
LOGGER.log(Level.SEVERE, "Error closing oiCache " + cache, e);
}
}
List dbNames = new ArrayList(databases.keySet());
for (String dbName: dbNames) try {
closeDatabase(dbName);
} catch (Exception e) {
LOGGER.log(Level.SEVERE, "Error closing db " + dbName, e);
}
try {
this.bdbEnvironment.sync();
} catch (Exception e) {
LOGGER.log(Level.SEVERE, "Error syncing when closing environment.", e);
}
try {
this.bdbEnvironment.close();
} catch (Exception e) {
LOGGER.log(Level.SEVERE, "Error closing environment.", e);
}
}
public Database getDatabase(String name) {
DatabasePlusConfig dpc = databases.get(name);
if (dpc == null) {
return null;
}
return dpc.database;
}
/** uniqueness serial number for temp map databases */
protected long sn = 0;
/**
* Creates a database-backed TempStoredSortedMap for transient
* reporting requirements. Calling the returned map's destroy()
* method when done discards the associated Database.
*
* @param
* @param
* @param dbName Database name to use; if null a name will be synthesized
* @param keyClass Class of keys; should be a Java primitive type
* @param valueClass Class of values; may be any serializable type
* @param allowDuplicates whether duplicate keys allowed
*/
public DisposableStoredSortedMap getStoredMap(String dbName, Class keyClass, Class valueClass, boolean allowDuplicates, boolean usePriorData) {
BdbConfig config = new BdbConfig();
config.setSortedDuplicates(allowDuplicates);
config.setAllowCreate(!usePriorData);
Database mapDb;
if(dbName==null) {
dbName = "tempMap-"+System.identityHashCode(this)+"-"+sn;
sn++;
}
final String openName = dbName;
try {
mapDb = openDatabase(openName,config,usePriorData);
} catch (DatabaseException e) {
throw new RuntimeException(e);
}
EntryBinding valueBinding = TupleBinding.getPrimitiveBinding(valueClass);
if(valueBinding == null) {
valueBinding = new SerialBinding(classCatalog, valueClass);
}
DisposableStoredSortedMap storedMap = new DisposableStoredSortedMap(
mapDb,
TupleBinding.getPrimitiveBinding(keyClass),
valueBinding,
true) {
@Override
public void dispose() {
super.dispose();
DatabasePlusConfig dpc = BdbModule.this.databases.remove(openName);
if (dpc == null) {
BdbModule.LOGGER.log(Level.WARNING,"No such database: " + openName);
}
}
};
return storedMap;
}
@Override
public void destroy() throws Exception {
close();
}
}
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