DataContextImpl(OptiqConnectionImpl connection, List<Object> parameterValues) {
this.queryProvider = connection;
this.typeFactory = connection.getTypeFactory();
this.rootSchema = connection.rootSchema;
// Store the time at which the query started executing. The SQL
// standard says that functions such as CURRENT_TIMESTAMP return the
// same value throughout the query.
final long time = System.currentTimeMillis();
final TimeZone timeZone = connection.getTimeZone();
final long localOffset = timeZone.getOffset(time);
final long currentOffset = localOffset;
ImmutableMap.Builder<Object, Object> builder = ImmutableMap.builder();
builder
.put("utcTimestamp", time)
.put("currentTimestamp", time + currentOffset)
.put("localTimestamp", time + localOffset)
.put("timeZone", timeZone);
for (Ord<Object> value : Ord.zip(parameterValues)) {
Object e = value.e;
if (e == null) {
e = AvaticaParameter.DUMMY_VALUE;
}
builder.put("?" + value.i, e);
}
map = builder.build();
}
/**
* collect saved Reflections resources from all urls that contains the given packagePrefix and
* matches the given resourceNameFilter and de-serializes them using the default serializer {@link
* XmlSerializer} or using the optionally supplied optionalSerializer
*
* <p>it is preferred to use a designated resource prefix (for example META-INF/reflections but
* not just META-INF), so that relevant urls could be found much faster
*
* @param optionalSerializer - optionally supply one serializer instance. if not specified or
* null, {@link XmlSerializer} will be used
*/
public static Reflections collect(
final String packagePrefix,
final Predicate<String> resourceNameFilter,
@Nullable Serializer... optionalSerializer) {
Serializer serializer =
optionalSerializer != null && optionalSerializer.length == 1
? optionalSerializer[0]
: new XmlSerializer();
Collection<URL> urls = ClasspathHelper.forPackage(packagePrefix);
if (urls.isEmpty()) return null;
long start = System.currentTimeMillis();
final Reflections reflections = new Reflections();
Iterable<Vfs.File> files = Vfs.findFiles(urls, packagePrefix, resourceNameFilter);
for (final Vfs.File file : files) {
InputStream inputStream = null;
try {
inputStream = file.openInputStream();
reflections.merge(serializer.read(inputStream));
} catch (IOException e) {
throw new ReflectionsException("could not merge " + file, e);
} finally {
close(inputStream);
}
}
if (log != null) {
Store store = reflections.getStore();
int keys = 0;
int values = 0;
for (String index : store.keySet()) {
keys += store.get(index).keySet().size();
values += store.get(index).size();
}
log.info(
format(
"Reflections took %d ms to collect %d url%s, producing %d keys and %d values [%s]",
System.currentTimeMillis() - start,
urls.size(),
urls.size() > 1 ? "s" : "",
keys,
values,
Joiner.on(", ").join(urls)));
}
return reflections;
}
public Builder setArguments(String[] arguments) {
checkNotNull(arguments, "arguments");
String[] newArguments = new String[arguments.length + 1];
newArguments[0] = "_";
System.arraycopy(arguments, 0, newArguments, 1, arguments.length);
this.arguments = newArguments;
return this;
}
public String[] getParsedPaddedSlice(int index, int padding) {
String[] slice = new String[parsedArgs.size() - index + padding];
System.arraycopy(
parsedArgs.toArray(new String[parsedArgs.size()]),
index,
slice,
padding,
parsedArgs.size() - index);
return slice;
}
public String[] getParsedSlice(int index) {
String[] slice = new String[parsedArgs.size() - index];
System.arraycopy(
parsedArgs.toArray(new String[parsedArgs.size()]),
index,
slice,
0,
parsedArgs.size() - index);
return slice;
}
public String printPendingRanges() {
StringBuilder sb = new StringBuilder();
for (Map.Entry<String, Multimap<Range, InetAddress>> entry : pendingRanges.entrySet()) {
for (Map.Entry<Range, InetAddress> rmap : entry.getValue().entries()) {
sb.append(rmap.getValue() + ":" + rmap.getKey());
sb.append(System.getProperty("line.separator"));
}
}
return sb.toString();
}
/**
* @param statsQuery StatisticsQueryCondition
* @param statisticsStorage
* @param scoringExps Set of experiments that have at least one non-zero score for
* statisticsQuery. This is used retrieving efos to be displayed in heatmap when no query efvs
* exist (c.f. atlasStatisticsQueryService.getScoringAttributesForGenes())
* @return experiment counts corresponding for statsQuery
*/
public static Multiset<Integer> getExperimentCounts(
StatisticsQueryCondition statsQuery,
StatisticsStorage statisticsStorage,
Set<ExperimentInfo> scoringExps) {
long start = System.currentTimeMillis();
Multiset<Integer> counts =
StatisticsQueryUtils.scoreQuery(statsQuery, statisticsStorage, scoringExps);
long dur = System.currentTimeMillis() - start;
int numOfGenesWithCounts = counts.elementSet().size();
if (numOfGenesWithCounts > 0) {
log.debug(
"StatisticsQuery: "
+ statsQuery.prettyPrint()
+ " ==> result set size: "
+ numOfGenesWithCounts
+ " (duration: "
+ dur
+ " ms)");
}
return counts;
}
/** Creates a JDBC data source with the given specification. */
public static DataSource dataSource(
String url, String driverClassName, String username, String password) {
if (url.startsWith("jdbc:hsqldb:")) {
// Prevent hsqldb from screwing up java.util.logging.
System.setProperty("hsqldb.reconfig_logging", "false");
}
BasicDataSource dataSource = new BasicDataSource();
dataSource.setUrl(url);
dataSource.setUsername(username);
dataSource.setPassword(password);
dataSource.setDriverClassName(driverClassName);
return dataSource;
}
@GET
@Path("/files")
public List<ToDo> files() {
List<ToDo> response = Lists.newArrayList();
File[] files = new File("/lib").listFiles();
if (files != null) {
for (File file : files) {
if (file.isFile())
response.add(
new ToDo(
++id,
file.getName(),
file.isFile() ? file.length() : -1,
System.currentTimeMillis()));
}
}
return response;
}
public String toString() {
StringBuilder sb = new StringBuilder();
lock.readLock().lock();
try {
Set<InetAddress> eps = tokenToEndPointMap.inverse().keySet();
if (!eps.isEmpty()) {
sb.append("Normal Tokens:");
sb.append(System.getProperty("line.separator"));
for (InetAddress ep : eps) {
sb.append(ep);
sb.append(":");
sb.append(tokenToEndPointMap.inverse().get(ep));
sb.append(System.getProperty("line.separator"));
}
}
if (!bootstrapTokens.isEmpty()) {
sb.append("Bootstrapping Tokens:");
sb.append(System.getProperty("line.separator"));
for (Map.Entry<Token, InetAddress> entry : bootstrapTokens.entrySet()) {
sb.append(entry.getValue() + ":" + entry.getKey());
sb.append(System.getProperty("line.separator"));
}
}
if (!leavingEndPoints.isEmpty()) {
sb.append("Leaving EndPoints:");
sb.append(System.getProperty("line.separator"));
for (InetAddress ep : leavingEndPoints) {
sb.append(ep);
sb.append(System.getProperty("line.separator"));
}
}
if (!pendingRanges.isEmpty()) {
sb.append("Pending Ranges:");
sb.append(System.getProperty("line.separator"));
sb.append(printPendingRanges());
}
} finally {
lock.readLock().unlock();
}
return sb.toString();
}
public static void main(final String[] args) {
int exitCode = 0;
try {
final Configuration configuration = new Configuration(true);
if (args.length == 1) {
configuration.addResource(new File(args[0]).toURI().toURL());
} else if (args.length > 1) {
throw new ExitSignal(1, "Usage: ./hadoop-repl <path-to-hadoop-core-site-file>");
}
new HadoopREPL(configuration).loop("hadoop> ");
} catch (final ExitSignal ex) {
System.err.println(ex.getMessage());
exitCode = ex.getExitCode();
} catch (final Exception ex) {
System.err.println(ex);
exitCode = 1;
}
System.exit(exitCode);
}
protected void scan() {
if (configuration.getUrls() == null || configuration.getUrls().isEmpty()) {
if (log != null) log.warn("given scan urls are empty. set urls in the configuration");
return;
}
if (log != null && log.isDebugEnabled()) {
log.debug("going to scan these urls:\n" + Joiner.on("\n").join(configuration.getUrls()));
}
long time = System.currentTimeMillis();
int scannedUrls = 0;
ExecutorService executorService = configuration.getExecutorService();
List<Future<?>> futures = Lists.newArrayList();
for (final URL url : configuration.getUrls()) {
try {
if (executorService != null) {
futures.add(
executorService.submit(
new Runnable() {
public void run() {
if (log != null && log.isDebugEnabled())
log.debug("[" + Thread.currentThread().toString() + "] scanning " + url);
scan(url);
}
}));
} else {
scan(url);
}
scannedUrls++;
} catch (ReflectionsException e) {
if (log != null && log.isWarnEnabled())
log.warn("could not create Vfs.Dir from url. ignoring the exception and continuing", e);
}
}
// todo use CompletionService
if (executorService != null) {
for (Future future : futures) {
try {
future.get();
} catch (Exception e) {
throw new RuntimeException(e);
}
}
}
time = System.currentTimeMillis() - time;
// gracefully shutdown the parallel scanner executor service.
if (executorService != null) {
executorService.shutdown();
}
if (log != null) {
int keys = 0;
int values = 0;
for (String index : store.keySet()) {
keys += store.get(index).keySet().size();
values += store.get(index).size();
}
log.info(
format(
"Reflections took %d ms to scan %d urls, producing %d keys and %d values %s",
time,
scannedUrls,
keys,
values,
executorService != null && executorService instanceof ThreadPoolExecutor
? format(
"[using %d cores]",
((ThreadPoolExecutor) executorService).getMaximumPoolSize())
: ""));
}
}
private void loadConfig() throws IOException, JedisConnectionException {
if (!getDataFolder().exists()) {
getDataFolder().mkdir();
}
File file = new File(getDataFolder(), "config.yml");
if (!file.exists()) {
file.createNewFile();
try (InputStream in = getResourceAsStream("example_config.yml");
OutputStream out = new FileOutputStream(file)) {
ByteStreams.copy(in, out);
}
}
final Configuration configuration =
ConfigurationProvider.getProvider(YamlConfiguration.class).load(file);
final String redisServer = configuration.getString("redis-server", "localhost");
final int redisPort = configuration.getInt("redis-port", 6379);
String redisPassword = configuration.getString("redis-password");
String serverId = configuration.getString("server-id");
if (redisPassword != null && (redisPassword.isEmpty() || redisPassword.equals("none"))) {
redisPassword = null;
}
// Configuration sanity checks.
if (serverId == null || serverId.isEmpty()) {
throw new RuntimeException("server-id is not specified in the configuration or is empty");
}
if (redisServer != null && !redisServer.isEmpty()) {
final String finalRedisPassword = redisPassword;
FutureTask<JedisPool> task =
new FutureTask<>(
new Callable<JedisPool>() {
@Override
public JedisPool call() throws Exception {
// With recent versions of Jedis, we must set the classloader to the one
// BungeeCord used
// to load RedisBungee with.
ClassLoader previous = Thread.currentThread().getContextClassLoader();
Thread.currentThread().setContextClassLoader(RedisBungee.class.getClassLoader());
// Create the pool...
JedisPoolConfig config = new JedisPoolConfig();
config.setMaxTotal(configuration.getInt("max-redis-connections", 8));
JedisPool pool =
new JedisPool(config, redisServer, redisPort, 0, finalRedisPassword);
// Reset classloader and return the pool
Thread.currentThread().setContextClassLoader(previous);
return pool;
}
});
getProxy().getScheduler().runAsync(this, task);
try {
pool = task.get();
} catch (InterruptedException | ExecutionException e) {
throw new RuntimeException("Unable to create Redis pool", e);
}
// Test the connection
try (Jedis rsc = pool.getResource()) {
rsc.ping();
// If that worked, now we can check for an existing, alive Bungee:
File crashFile = new File(getDataFolder(), "restarted_from_crash.txt");
if (crashFile.exists()) {
crashFile.delete();
} else if (rsc.hexists("heartbeats", serverId)) {
try {
long value = Long.parseLong(rsc.hget("heartbeats", serverId));
if (System.currentTimeMillis() < value + 20000) {
getLogger()
.severe(
"You have launched a possible impostor BungeeCord instance. Another instance is already running.");
getLogger()
.severe("For data consistency reasons, RedisBungee will now disable itself.");
getLogger()
.severe(
"If this instance is coming up from a crash, create a file in your RedisBungee plugins directory with the name 'restarted_from_crash.txt' and RedisBungee will not perform this check.");
throw new RuntimeException("Possible impostor instance!");
}
} catch (NumberFormatException ignored) {
}
}
FutureTask<Void> task2 =
new FutureTask<>(
new Callable<Void>() {
@Override
public Void call() throws Exception {
httpClient = new OkHttpClient();
Dispatcher dispatcher = new Dispatcher(getExecutorService());
httpClient.setDispatcher(dispatcher);
NameFetcher.setHttpClient(httpClient);
UUIDFetcher.setHttpClient(httpClient);
RedisBungee.configuration =
new RedisBungeeConfiguration(RedisBungee.this.getPool(), configuration);
return null;
}
});
getProxy().getScheduler().runAsync(this, task2);
try {
task2.get();
} catch (InterruptedException | ExecutionException e) {
throw new RuntimeException("Unable to create HTTP client", e);
}
getLogger().log(Level.INFO, "Successfully connected to Redis.");
} catch (JedisConnectionException e) {
pool.destroy();
pool = null;
throw e;
}
} else {
throw new RuntimeException("No redis server specified!");
}
}
@Override
public void onEnable() {
try {
loadConfig();
} catch (IOException e) {
throw new RuntimeException("Unable to load/save config", e);
} catch (JedisConnectionException e) {
throw new RuntimeException("Unable to connect to your Redis server!", e);
}
if (pool != null) {
try (Jedis tmpRsc = pool.getResource()) {
// This is more portable than INFO <section>
String info = tmpRsc.info();
for (String s : info.split("\r\n")) {
if (s.startsWith("redis_version:")) {
String version = s.split(":")[1];
if (!(usingLua = RedisUtil.canUseLua(version))) {
getLogger()
.warning(
"Your version of Redis ("
+ version
+ ") is not at least version 2.6. RedisBungee requires a newer version of Redis.");
throw new RuntimeException("Unsupported Redis version detected");
} else {
LuaManager manager = new LuaManager(this);
serverToPlayersScript =
manager.createScript(
IOUtil.readInputStreamAsString(
getResourceAsStream("lua/server_to_players.lua")));
getPlayerCountScript =
manager.createScript(
IOUtil.readInputStreamAsString(
getResourceAsStream("lua/get_player_count.lua")));
getServerPlayersScript =
manager.createScript(
IOUtil.readInputStreamAsString(
getResourceAsStream("lua/get_server_players.lua")));
}
break;
}
}
tmpRsc.hset(
"heartbeats", configuration.getServerId(), String.valueOf(System.currentTimeMillis()));
long uuidCacheSize = tmpRsc.hlen("uuid-cache");
if (uuidCacheSize > 750000) {
getLogger()
.info(
"Looks like you have a really big UUID cache! Run https://www.spigotmc.org/resources/redisbungeecleaner.8505/ as soon as possible.");
}
}
serverIds = getCurrentServerIds(true, false);
uuidTranslator = new UUIDTranslator(this);
heartbeatTask =
getProxy()
.getScheduler()
.schedule(
this,
new Runnable() {
@Override
public void run() {
try (Jedis rsc = pool.getResource()) {
long redisTime = getRedisTime(rsc.time());
rsc.hset(
"heartbeats", configuration.getServerId(), String.valueOf(redisTime));
} catch (JedisConnectionException e) {
// Redis server has disappeared!
getLogger()
.log(
Level.SEVERE,
"Unable to update heartbeat - did your Redis server go away?",
e);
}
serverIds = getCurrentServerIds(true, false);
globalPlayerCount.set(getCurrentCount());
}
},
0,
3,
TimeUnit.SECONDS);
dataManager = new DataManager(this);
if (configuration.isRegisterBungeeCommands()) {
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.GlistCommand(this));
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.FindCommand(this));
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.LastSeenCommand(this));
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.IpCommand(this));
}
getProxy().getPluginManager().registerCommand(this, new RedisBungeeCommands.SendToAll(this));
getProxy().getPluginManager().registerCommand(this, new RedisBungeeCommands.ServerId(this));
getProxy().getPluginManager().registerCommand(this, new RedisBungeeCommands.ServerIds());
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.PlayerProxyCommand(this));
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.PlistCommand(this));
getProxy()
.getPluginManager()
.registerCommand(this, new RedisBungeeCommands.DebugCommand(this));
api = new RedisBungeeAPI(this);
getProxy()
.getPluginManager()
.registerListener(
this, new RedisBungeeListener(this, configuration.getExemptAddresses()));
getProxy().getPluginManager().registerListener(this, dataManager);
psl = new PubSubListener();
getProxy().getScheduler().runAsync(this, psl);
integrityCheck =
getProxy()
.getScheduler()
.schedule(
this,
new Runnable() {
@Override
public void run() {
try (Jedis tmpRsc = pool.getResource()) {
Set<String> players = getLocalPlayersAsUuidStrings();
Set<String> playersInRedis =
tmpRsc.smembers(
"proxy:" + configuration.getServerId() + ":usersOnline");
List<String> lagged = getCurrentServerIds(false, true);
// Clean up lagged players.
for (String s : lagged) {
Set<String> laggedPlayers =
tmpRsc.smembers("proxy:" + s + ":usersOnline");
tmpRsc.del("proxy:" + s + ":usersOnline");
if (!laggedPlayers.isEmpty()) {
getLogger()
.info(
"Cleaning up lagged proxy "
+ s
+ " ("
+ laggedPlayers.size()
+ " players)...");
for (String laggedPlayer : laggedPlayers) {
RedisUtil.cleanUpPlayer(laggedPlayer, tmpRsc);
}
}
}
for (Iterator<String> it = playersInRedis.iterator(); it.hasNext(); ) {
String member = it.next();
if (!players.contains(member)) {
// Are they simply on a different proxy?
String found = null;
for (String proxyId : getServerIds()) {
if (proxyId.equals(configuration.getServerId())) continue;
if (tmpRsc.sismember("proxy:" + proxyId + ":usersOnline", member)) {
// Just clean up the set.
found = proxyId;
break;
}
}
if (found == null) {
RedisUtil.cleanUpPlayer(member, tmpRsc);
getLogger()
.warning(
"Player found in set that was not found locally and globally: "
+ member);
} else {
tmpRsc.srem(
"proxy:" + configuration.getServerId() + ":usersOnline", member);
getLogger()
.warning(
"Player found in set that was not found locally, but is on another proxy: "
+ member);
}
it.remove();
}
}
Pipeline pipeline = tmpRsc.pipelined();
for (String player : players) {
if (playersInRedis.contains(player)) continue;
// Player not online according to Redis but not BungeeCord.
getLogger()
.warning("Player " + player + " is on the proxy but not in Redis.");
ProxiedPlayer proxiedPlayer =
ProxyServer.getInstance().getPlayer(UUID.fromString(player));
if (proxiedPlayer == null) continue; // We'll deal with it later.
RedisUtil.createPlayer(proxiedPlayer, pipeline, true);
}
pipeline.sync();
}
}
},
0,
1,
TimeUnit.MINUTES);
}
getProxy().registerChannel("RedisBungee");
}
public String[] getPaddedSlice(int index, int padding) {
String[] slice = new String[originalArgs.length - index + padding];
System.arraycopy(originalArgs, index, slice, padding, originalArgs.length - index);
return slice;
}
public String[] getSlice(int index) {
String[] slice = new String[originalArgs.length - index];
System.arraycopy(originalArgs, index, slice, 0, originalArgs.length - index);
return slice;
}