It's JBoss AS 7.1.1.Final

In my standalone.xml I have

        <subsystem xmlns="urn:jboss:domain:datasources:1.0">
            <datasources>
                <datasource jndi-name="java:/my/DS1" pool-name="My1" enabled="true" use-java-context="true">
                    <connection-url>jdbc:oracle:thin:@10.172.1.1:1521:ABCD</connection-url>
                    <driver>oracle</driver>
                    <pool>
                        <min-pool-size>1</min-pool-size>
                        <max-pool-size>10</max-pool-size>
                        <prefill>true</prefill>
                        <use-strict-min>false</use-strict-min>
                    </pool>
                    <security>
                        <user-name>xxx</user-name>
                        <password>xxx</password>
                    </security>
                    <timeout>
                        <idle-timeout-minutes>5</idle-timeout-minutes>
                    </timeout>
                    <statement>
                        <prepared-statement-cache-size>500</prepared-statement-cache-size>
                        <share-prepared-statements>true</share-prepared-statements>
                    </statement>
                </datasource>
                    <drivers>
                    <driver name="oracle" module="com.oracle"/>
                </drivers>
            </datasources>
        </subsystem>

then, I lookup the datasources in the code:

{code:java}
DataSource ds = new InitialContext().lookup("java:/my/DS1");
JdbcTemplate jdbcTemplate = new JdbcTemplate(dataSource);
{code}

The datasource has to be looked up programmatically and not hard-coded in spring.xml since there can be multiple data sources and their JNDI names are configured in external properties file that the application scans on startup.

Then, the jdbcTemplate is passed to a TableScanner that is invoked with Spring scheduling:

{code:java}
    public TableScanner(JdbTemplate jdbcTemplate) {
        this.jdbcTemplate = jdbcTemplate;
    }
 
    @Scheduled(fixedDelay = 5000)
    public void run() {
        // query a table using jdbcTemplate and process the retrieved records, deleting them at the end of processing
    }
{code}

When stopping of the server occurs during run() method invocation, all the retrieved records should be processed and deleted. When the application tries to delete them, the connection manager is already closed, hence the exception.

The whole log from the shutdown is:

{code}
14:31:51,604 INFO  [org.jboss.as.logging] JBAS011503: Restored bootstrap log handlers
14:31:51,617 INFO  [org.apache.coyote.http11.Http11Protocol] Stopping Coyote HTTP/1.1 on http-127.0.0.1-127.0.0.1-18080
14:31:51,638 INFO  [org.hornetq.ra.HornetQResourceAdapter] HornetQ resource adapter stopped
14:31:51,653 INFO  [org.apache.catalina.core.ContainerBase.[jboss.web].[default-host].[/MY-APP]] Closing Spring root WebApplicationContext
14:31:51,656 INFO  [org.springframework.web.context.support.XmlWebApplicationContext] Closing Root WebApplicationContext: startup date [Tue Jul 09 14:30:56 CST 2013]; root of context hierarchy
14:31:51,659 INFO  [org.springframework.beans.factory.support.DefaultListableBeanFactory] Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2c591927: defining beans [<snipped>]; root of factory hierarchy
14:31:51,662 INFO  [org.hornetq.core.server.impl.HornetQServerImpl] HornetQ Server version 2.2.13.Final (HQ_2_2_13_FINAL_AS7, 122) [5f713ff6-5f86-11e2-a25d-1f3857764d50] stopped
14:31:51,673 INFO  [MY-APP.Shutdown] Initializing shutdown. Already running tasks will be finished, new tasks will not be executed.
14:31:53,626 ERROR [org.springframework.scheduling.support.TaskUtils$LoggingErrorHandler] Unexpected error occurred in scheduled task.: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is java.sql.SQLException: javax.resource.ResourceException: IJ000451: The connection manager is shutdown: java:/my/DS1
    at org.springframework.jdbc.datasource.DataSourceUtils.getConnection(DataSourceUtils.java:80) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:575) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:818) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:874) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:882) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at com.my.app.scanner.db.SyncEntryRepository.deleteById(SyncEntryRepository.java:26) [classes:]
    at com.my.app.rules.orphanentries.OrphanedEntriesProcessor.process(OrphanedEntriesProcessor.java:22) [classes:]
    at com.my.app.routing.Router$RoutingWorker.performRouting(Router.java:49) [classes:]
    at com.my.app.routing.Router$RoutingWorker.route(Router.java:32) [classes:]
    at com.my.app.routing.Router.route(Router.java:18) [classes:]
    at com.my.app.transformation.Transformation.perform(Transformation.java:21) [classes:]
    at com.my.app.MyApp.run(MyApp.java:18) [classes:]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [rt.jar:1.6.0_45]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [rt.jar:1.6.0_45]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [rt.jar:1.6.0_45]
    at java.lang.reflect.Method.invoke(Method.java:597) [rt.jar:1.6.0_45]
    at org.springframework.scheduling.support.ScheduledMethodRunnable.run(ScheduledMethodRunnable.java:64) [spring-context-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:53) [spring-context-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439) [rt.jar:1.6.0_45]
    at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317) [rt.jar:1.6.0_45]
    at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150) [rt.jar:1.6.0_45]
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(ScheduledThreadPoolExecutor.java:98) [rt.jar:1.6.0_45]
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(ScheduledThreadPoolExecutor.java:180) [rt.jar:1.6.0_45]
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:204) [rt.jar:1.6.0_45]
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) [rt.jar:1.6.0_45]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) [rt.jar:1.6.0_45]
    at java.lang.Thread.run(Thread.java:662) [rt.jar:1.6.0_45]
Caused by: java.sql.SQLException: javax.resource.ResourceException: IJ000451: The connection manager is shutdown: java:/my/DS1
    at org.jboss.jca.adapters.jdbc.WrapperDataSource.getConnection(WrapperDataSource.java:137)
    at org.springframework.jdbc.datasource.DataSourceUtils.doGetConnection(DataSourceUtils.java:111) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    at org.springframework.jdbc.datasource.DataSourceUtils.getConnection(DataSourceUtils.java:77) [spring-jdbc-3.2.3.RELEASE.jar:3.2.3.RELEASE]
    ... 26 more
Caused by: javax.resource.ResourceException: IJ000451: The connection manager is shutdown: java:/my/DS1
    at org.jboss.jca.core.connectionmanager.AbstractConnectionManager.getManagedConnection(AbstractConnectionManager.java:321)
    at org.jboss.jca.core.connectionmanager.tx.TxConnectionManagerImpl.getManagedConnection(TxConnectionManagerImpl.java:368)
    at org.jboss.jca.core.connectionmanager.AbstractConnectionManager.allocateConnection(AbstractConnectionManager.java:464)
    at org.jboss.jca.adapters.jdbc.WrapperDataSource.getConnection(WrapperDataSource.java:129)
    ... 28 more
 
14:31:53,640 INFO  [MY-APP.Shutdown] Shutdown complete
14:31:53,651 INFO  [org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean] Closing JPA EntityManagerFactory for persistence unit 'default'
14:31:53,656 INFO  [org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean] Closing JPA EntityManagerFactory for persistence unit 'default'
14:31:53,837 INFO  [org.jboss.as.server.deployment] JBAS015877: Stopped deployment MY-APP.war in 2259ms
14:31:56,158 INFO  [com.arjuna.ats.jbossatx] ARJUNA032018: Destroying TransactionManagerService
14:31:56,158 INFO  [com.arjuna.ats.jbossatx] ARJUNA032014: Stopping transaction recovery manager
14:31:56,160 INFO  [org.jboss.as] JBAS015950: JBoss AS 7.1.1.Final "Brontes" stopped in 4567ms
{code}

I found this JBoss AS issue, which reflects my problem. It appears that if the data sources are not bound in a static way, via @Resource, then the server does not know that the data source is still in use. I went with letting Spring manage the data sources on its own, which may not be the Java EE way, but gets the work done and is appropriate in my situation.

Yes, unfortunately the WFLY-944 bug workaround suggests the same. In my case this does not help since I need to use the data sources whose JNDI names are listed in my application's properties file, so they cannot be hard-coded neither as @Resource nor in web.xml. I ended up letting Spring manage the data sources instead of JBoss AS. Not the JEE way, but it worked in my case.