Posts Tagged ‘Java’
How to Read a BLOB for a Human Being?
Case
I have had to access a BLOB and read its content. By principle, I dislike using binary objects, which do not suit easy tracing and auditing. Anyway, in my case, floats are stored in a BLOB, and I need read them in order to validate my current development.
You have many ways to read the content of the BLOB. I used two: SQL and Java
SQL
Start your TOAD for Oracle ; you can launch queries similar to this:
SELECT UTL_RAW.cast_to_binary_float
(DBMS_LOB.submyrecord (myrecord.myrecordess,
4,
1 + (myrecordessnameid * 4)
)
) AS myrecordessvalue
FROM mytable myrecord
WHERE myrecordessid = 123456;
You can also run a stored procedure, similar to this:
DECLARE
blobAsVariable BLOB;
my_vr RAW (4);
blobValue FLOAT;
bytelen NUMBER := 4;
v_index NUMBER := 5;
jonathan RAW (4);
loopLength INT;
BEGIN
SELECT myField
INTO blobAsVariable
FROM myTable
WHERE tableid = (5646546846);
DBMS_LOB.READ (blobAsVariable, bytelen, 1, jonathan);
loopLength := UTL_RAW.cast_to_binary_integer (jonathan);
FOR rec IN 1 .. loopLength
LOOP
DBMS_LOB.READ (blobAsVariable, bytelen, v_index, my_vr);
blobValue := UTL_RAW.cast_to_binary_float (my_vr);
v_index := v_index + 4;
DBMS_OUTPUT.put_line (TO_CHAR (blobValue));
END LOOP;
END;
Java
I am still not sure to be DBA expert. Indeed I am convinced I am more fluent in Java than in PL/SQL 😉
Create a Spring configuration file, let’s say BlobRuntimeTest-applicationContext.xml:
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
xmlns:tx="http://www.springframework.org/schema/tx"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd">
<!-- $Id: BlobRuntimeTest-applicationContext.xml $ -->
<bean id="dataSource" destroy-method="close" class="org.apache.commons.dbcp.BasicDataSource">
<property name="driverClassName" value="oracle.jdbc.driver.OracleDriver"/>
<property name="url" value="jdbc:oracle:thin:@myDBserver:1234:MY_SCHEMA"/>
<property name="username" value="jonathan"/>
<property name="password" value="lalou"/>
<property name="initialSize" value="2"/>
<property name="minIdle" value="2"/>
</bean>
<bean id="jdbcTemplate" class="org.springframework.jdbc.core.JdbcTemplate">
<property name="dataSource" ref="dataSource"/>
</bean>
</beans>
Now create a runtime test:
/**
* User: Jonathan Lalou
* Date: Aug 7, 2011
* Time: 5:22:33 PM
* $Id: BlobRuntimeTest.java $
*/
public class BlobRuntimeTest extends TestCase {
private static final Logger LOGGER = Logger.getLogger(BlobRuntimeTest.class);
private static final String TABLE = "jonathanTable";
private static final String PK_FIELD = "jonathanTablePK";
private static final String BLOB_FIELD = "myBlobField";
private static final int[] PK_VALUES = {123, 456, 789};
private ApplicationContext applicationContext;
private JdbcTemplate jdbcTemplate;
@Before
public void setUp() throws Exception {
applicationContext = new ClassPathXmlApplicationContext(
"lalou/jonathan/the/cownboy/BlobRuntimeTest-applicationContext.xml");
assertNotNull(applicationContext);
jdbcTemplate = (JdbcTemplate) applicationContext.getBean("jdbcTemplate");
assertNotNull(jdbcTemplate);
}
@After
public void tearDown() throws Exception {
}
@Test
public void testGetArray() throws Exception {
for (int pk_value : PK_VALUES) {
final Blob blob;
final byte[] bytes;
final float[] floats;
blob = (Blob) jdbcTemplate.queryForObject("select " + BLOB_FIELD + " from " + TABLE + " where " + PK_FIELD + " = " + pk_value, Blob.class);
assertNotNull(blob);
bytes = blob.getBytes(1, (int) blob.length());
// process your blob: unzip, read, concat, add, etc..
// floats = ....
LOGGER.info("Blob size: " + floats.length);
LOGGER.info(ToStringBuilder.reflectionToString(floats));
}
}
}
Thread leaks in Mule ESB 2.2.1
Abstract
The application I work on packages Mule ESB 2.2.1 in a WAR and deploys it under a WebLogic 10.3 server. My team mates and I noticed that, on multiple deploy/undeploy cycles, the PermGen size dramatically decreased. The cause of this was the number of threads, which hardly decreased on undeployment phases, unlike the expected behaviour.
Indeed, Mule is seldom deployed as a WebApp. Rather, it is designed to be run as a standalone application, within a Tanuki wrapper. When the JVM is killed, all the threads are killed, too, and therefore no thread survives ; hence, the memory is freed and there is no reason to fear a thread leak.
Moreover, when the application is redeployed, new threads -with the same names as the “old” threads- are created. The risk is that, for any reason, a thread-name-based communication between threads may fail, because the communication pipe may be read by the wrong thread.
In my case: on WebLogic startup, there are 31 threads ; when the application is deployed, there are 150 ; when the application works (receives and handles messages), the number of threads climbs to 800 ; when the application is undeployed, only 12 threads are killed, the other remaining alive.
The question is: how to kill Mule-created threads, in order to avoid a Thread leak?
WebLogic Threads
I performed a thread dump at WebLogic startup. Here are WebLogic threads, created before any deployment occurs:
Attach Listener DoSManager DynamicListenThread[Default[1]] DynamicListenThread[Default] ExecuteThread: '0' for queue: 'weblogic.socket.Muxer' ExecuteThread: '1' for queue: 'weblogic.socket.Muxer' ExecuteThread: '2' for queue: 'weblogic.socket.Muxer' Finalizer JMX server connection timeout 42 RMI Scheduler(0) RMI TCP Accept-0 RMI TCP Connection(1)-127.0.0.1 RMI TCP Connection(2)-127.0.0.1 Reference Handler Signal Dispatcher Thread-10 Thread-11 Timer-0 Timer-1 VDE Transaction Processor Thread [ACTIVE] ExecuteThread: '0' for queue: 'weblogic.kernel.Default (self-tuning)' [ACTIVE] ExecuteThread: '2' for queue: 'weblogic.kernel.Default (self-tuning)' [STANDBY] ExecuteThread: '1' for queue: 'weblogic.kernel.Default (self-tuning)' [STANDBY] ExecuteThread: '3' for queue: 'weblogic.kernel.Default (self-tuning)' [STANDBY] ExecuteThread: '4' for queue: 'weblogic.kernel.Default (self-tuning)' [STANDBY] ExecuteThread: '5' for queue: 'weblogic.kernel.Default (self-tuning)' main weblogic.GCMonitor weblogic.cluster.MessageReceiver weblogic.time.TimeEventGenerator weblogic.timers.TimerThread
Dispose Disposables, Stop Stoppables…
The application being deployed in a WAR, I created a servlet implementing ServletContextListener. In the method contextDestroyed(), I destroy Mule objects (Disposable, Stoppable, Model, Service, etc.) one per one.
Eg#1:
final Collection<Model> allModels;
try {
allModels = MuleServer.getMuleContext().getRegistry().lookupObjects(Model.class);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Disposing models " + allModels.size());
}
for (Model model : allModels) {
model.dispose();
}
allModels.clear();
} catch (Exception e) {
LOGGER.error(e);
}
Eg#2:
private void stopStoppables() {
final Collection<Stoppable> allStoppables;
try {
allStoppables = MuleServer.getMuleContext().getRegistry().lookupObjects(Stoppable.class);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Stopping stoppables " + allStoppables.size());
}
for (Stoppable stoppable : allStoppables) {
stoppable.stop();
}
allStoppables.clear();
} catch (MuleException e) {
LOGGER.error(e);
}
}
This first step is needed because default mechanism is flawed: Mule re-creates objects that were destroyed.
Kill Threads
The general idea to kill Mule threads is the following: perform a Unix-style “diff” between WebLogic native threads, and the threads still alive once all Mule objects have been stopped and disposed.
On Application Startup
In the ServletContextListener, I add a field that will be set in a method called in the constructor:
private List<String> threadsAtStartup;
(...)
/**
* This method retrieves the Threads present at startup: mainly speaking, they are Threads related to WebLogic.
*/
private void retrieveThreadsOnStartup() {
final Thread[] threads;
final ThreadGroup threadGroup;
threadGroup = Thread.currentThread().getThreadGroup();
try {
threads = retrieveCurrentActiveThreads(threadGroup);
} catch (NoSuchFieldException e) {
LOGGER.error("Could not retrieve initial Threads list. The application may be unstable on shutting down ", e);
threadsAtStartup = new ArrayList<String>();
return;
} catch (IllegalAccessException e) {
LOGGER.error("Could not retrieve initial Threads list. The application may be unstable on shutting down ", e);
threadsAtStartup = new ArrayList<String>();
return;
}
threadsAtStartup = new ArrayList<String>(threads.length);
for (int i = 0; i < threads.length; i++) {
final Thread thread;
try {
thread = threads[i];
if (null != thread) {
threadsAtStartup.add(thread.getName());
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("This Thread was available at startup: " + thread.getName());
}
}
} catch (RuntimeException e) {
LOGGER.error("An error occured on initial Thread statement: ", e);
}
}
}
/**
* Hack to retrieve the field ThreadGroup.threads, which is package-protected and therefore not accessible
*
* @param threadGroup
* @return
* @throws NoSuchFieldException
* @throws IllegalAccessException
*/
private Thread[] retrieveCurrentActiveThreads(ThreadGroup threadGroup) throws NoSuchFieldException, IllegalAccessException {
final Thread[] threads;
final Field privateThreadsField;
privateThreadsField = ThreadGroup.class.getDeclaredField("threads");
privateThreadsField.setAccessible(true);
threads = (Thread[]) privateThreadsField.get(threadGroup);
return threads;
}
On application shutdown
In the method ServletContextListener.contextDestroyed(), let’s call this method:
/**
* Cleanses the Threads on shutdown: theorically, when the WebApp is undeployed, should remain only the threads
* that were present before the WAR was deployed. Unfornately, Mule leaves alive many threads on shutdown, reducing
* PermGen size and recreating new threads with the same names as the old ones, inducing a kind of instability.
*/
private void cleanseThreadsOnShutdown() {
final Thread[] threads;
final ThreadGroup threadGroup;
final String currentThreadName;
currentThreadName = Thread.currentThread().getName();
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("On shutdown, currentThreadName is: " + currentThreadName);
}
threadGroup = Thread.currentThread().getThreadGroup();
try {
threads = retrieveCurrentActiveThreads(threadGroup);
} catch (NoSuchFieldException e) {
LOGGER.error("An error occured on Threads cleaning at shutdown", e);
return;
} catch (IllegalAccessException e) {
LOGGER.error("An error occured on Threads cleaning at shutdown", e);
return;
}
for (Thread thread : threads) {
final String threadName = thread.getName();
final Boolean shouldThisThreadBeKilled;
shouldThisThreadBeKilled = isThisThreadToBeKilled(currentThreadName, threadName);
if (LOGGER.isDebugEnabled()) {
LOGGER.info("should the thread named " + threadName + " be killed? " + shouldThisThreadBeKilled);
}
if (shouldThisThreadBeKilled) {
thread.interrupt();
thread = null;
}
}
}
/**
* Says whether a thread is to be killed<br/>
* Rules:
* <ul><li>a Thread must NOT be killed if:</li>
* <ol>
* <li>it was among the threads available at startup</li>
* <li>it is a Thread belonging to WebLogic (normally, WebLogic threads are among the list in the previous case</li>
* <li>it is the current Thread (simple protection against unlikely situation)</li>
* </ol>
* <li>a Thread must be killed: in all other cases</li>
* </ul>
*
* @param currentThreadName
* @param threadName
* @return
*/
private Boolean isThisThreadToBeKilled(String currentThreadName, String threadName) {
final Boolean toBeKilled;
toBeKilled = !threadsAtStartup.contains(threadName)
&& !StringUtils.contains(threadName, "weblogic")
&& !threadName.equalsIgnoreCase(currentThreadName);
return toBeKilled;
}
EhCache
My application uses an EhCache. Its threads names usually end with “.data”. They are not killed by the previous actions. To get rid of them, the most elegant way is to add this block in the web.xml:
<listener>
<listener-class>net.sf.ehcache.constructs.web.ShutdownListener</listener-class>
</listener>
With all these operations, almost all threads are killed. But Java VisualVM still displays 34, vs. 31 at startup.
Tough Threads
A thread dump confirms that, at this point, 3 rebellious threads still refuse to be kill:
MuleServer.1 SocketTimeoutMonitor-Monitor.1 SocketTimeoutMonitor-Monitor.1
Let’s examine them:
MuleServer.1: This thread is an instance of the inner classMuleServer.ShutdownThread. Indeed, this is the first thread created by Mule, and therefore appears among the threads available at startup, before theServletContextListeneris called… I did not succeed in killing it, even why trying to kill it namely, which makes sense: killing the father thread looks like suiciding theServletContextListener.SocketTimeoutMonitor-Monitor.1: This thread is created by Mule’sTcpConnectorand its daughter classes:HttpConnector,SslConnector, etc. Again, I could not kill them.
Conclusion
We have seen Mule suffers of major thread leaks when deployed as a WAR. Anyway, most of these leaks may be sealed.
I assume MuleSoft was aware of this issue: in the version 3 of Mule, the deployment of webapps was refactored.
How to access non-visible fields in Java?
How to access a non-acccessible field (either protected, package-protected or private) of an object in Java?
For instance, you would like to access the field threads of ThreadGroup:
ThreadGroup threadGroup = Thread.currentThread().getThreadGroup(); final Field privateThreadsField; privateThreadsField = ThreadGroup.class.getDeclaredField("threads"); privateThreadsField.setAccessible(true); threads = (Thread[]) privateThreadsField.get(threadGroup);
How to include a dependency to tools.jar in Maven?
Case
You need include tools.jar as a dependency in a pom.xml, for instance in order to use Java 5’s annotations and APT. From a “Maven’s view point”, tools.jar is not a regular JAR defined by a groupId and artefactId.
Solution
Add this block in your pom.xml:
<dependency>
<groupId>com.sun</groupId>
<artifactId>tools</artifactId>
<version>1.6.0_24</version>
<scope>system</scope>
<systemPath>${java.home}/../lib/tools.jar</systemPath>
</dependency>
(You can also add it in your settings.xml)
You can do the same for any other “non-regular” JAR, available in your file system.
javac: invalid flag: -s
Case
After updating my project and launching a build with Maven, I got this error:
[ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Compilation failure Failure executing javac, but could not parse the error: javac: invalid flag: -s Usage: javac <options> <source files>
Fix
Indeed the version of Java in the pom.xml had been upgraded. To get rid of the error, update your $JAVA_HOME to use a JDK 6 and no more a JDK5.