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InterProScan JMS Implementation Module
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<beans
xmlns="http://www.springframework.org/schema/beans"
xmlns:amq="http://activemq.apache.org/schema/core"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.2.xsd
http://activemq.apache.org/schema/core http://activemq.apache.org/schema/core/activemq-core-5.12.0.xsd">
<import resource="classpath:/spring/spring-properties-context.xml"/>
<import resource="classpath:/spring/jobs/all-jobs-context.xml"/>
<!--<import resource="classpath:/spring/jms/activemq/activemq-queue-config-context.xml"/>-->
<import resource="classpath:/spring/jms/activemq/activemq-inVm-connection-config-context.xml"/>
<import resource="classpath:/spring/jms/activemq/activemq-remote-connection-config-context.xml"/>
<!--TODO: This is already defined in the activemg broker context file-->
<!-- Embedded ActiveMQ Broker - in vm connections only· -->
<amq:broker
id="jmsBroker"
useJmx="false"
persistent="false"
useShutdownHook="false"
start="false"
dedicatedTaskRunner="false"
tmpDataDirectory="${jms.broker.temp.directory}">
<amq:plugins>
<amq:statisticsBrokerPlugin id="stats"/>
</amq:plugins>
<amq:systemUsage>
<amq:systemUsage>
<amq:memoryUsage>
<amq:memoryUsage limit="1024 mb"/>
</amq:memoryUsage>
<!--<amq:storeUsage>-->
<!--<amq:storeUsage limit="1 gb"/>-->
<!--</amq:storeUsage>-->
<amq:tempUsage>
<amq:tempUsage limit="100 mb"/>
</amq:tempUsage>
</amq:systemUsage>
</amq:systemUsage>
<amq:transportConnectors>
<amq:transportConnector uri="vm://localhost?create=false"/>
</amq:transportConnectors>
</amq:broker>
<!-- start config to refactor-->
<!--<!– Local (e.g. vm) JMS ConnectionFactory –>-->
<!--<!– JMS ConnectionFactory to use, configuring the embedded broker using XML –>-->
<!--<amq:connectionFactory-->
<!--id="localJmsFactory"-->
<!--useCompression="false"-->
<!--optimizeAcknowledge="true"-->
<!--brokerURL="vm://localhost?create=false"-->
<!--alwaysSessionAsync="false"-->
<!--exceptionListener="#workerExceptionListener"-->
<!--transportListener="#workerTransportListener">-->
<!--<amq:prefetchPolicy>-->
<!--<amq:prefetchPolicy queuePrefetch="1"/>-->
<!--</amq:prefetchPolicy>-->
<!--</amq:connectionFactory>-->
<!--<!– JMS Error handler–>-->
<!--<bean id="jmsErrorHandler" class="uk.ac.ebi.interpro.scan.jms.activemq.JMSErrorHandler" />-->
<!--<!– JMS Exception handler–>-->
<!--<bean id="jmsIOExceptionHandler" class="uk.ac.ebi.interpro.scan.jms.activemq.JMSIOExceptionHandler" />-->
<!--<!– JMS transport Listener–>-->
<!--<bean id="workerTransportListener" class="uk.ac.ebi.interpro.scan.jms.activemq.JMSTransportListener" />-->
<!--<!– JMS Exception Listener–>-->
<!--<bean id="workerExceptionListener" class="uk.ac.ebi.interpro.scan.jms.activemq.JMSExceptionListener" >-->
<!--<property name="controller" ref="distributedWorkerController"/>-->
<!--</bean>-->
<!--<!– Local Spring JMSTemplate –>-->
<!--<bean id="localJmsTemplate" class="org.springframework.jms.core.JmsTemplate">-->
<!--<property name="connectionFactory">-->
<!--<bean class="org.springframework.jms.connection.CachingConnectionFactory">-->
<!--<constructor-arg ref="localJmsFactory"/>-->
<!--<property name="sessionCacheSize" value="100"/>-->
<!--</bean>-->
<!--</property>-->
<!--<property name="explicitQosEnabled" value="true"/>-->
<!--<property name="sessionAcknowledgeModeName" value="CLIENT_ACKNOWLEDGE"/>-->
<!--</bean>-->
<!--<!– Local Spring JMSTopicTemplate –>-->
<!--<bean id="jmsTopicTemplate" class="org.springframework.jms.core.JmsTemplate">-->
<!--<property name="connectionFactory">-->
<!--<bean class="org.springframework.jms.connection.CachingConnectionFactory">-->
<!--<constructor-arg ref="localJmsFactory"/>-->
<!--</bean>-->
<!--</property>-->
<!--<property name="pubSubDomain" value="true"/>-->
<!--</bean>-->
<!--<!– Remote (e.g. TCP) JMS ConnectionFactory –>-->
<!--<amq:connectionFactory-->
<!--id="remoteJmsFactory"-->
<!--useCompression="true"-->
<!--optimizeAcknowledge="true"-->
<!--alwaysSessionAsync="false"-->
<!--brokerURL="vm://localhost?create=false">-->
<!--<amq:prefetchPolicy>-->
<!--<amq:prefetchPolicy queuePrefetch="1"/>-->
<!--</amq:prefetchPolicy>-->
<!--</amq:connectionFactory>-->
<!--<!– Remote Spring JMSTemplate –>-->
<!--<bean id="remoteJmsTemplate" class="org.springframework.jms.core.JmsTemplate">-->
<!--<property name="connectionFactory">-->
<!--<bean class="org.springframework.jms.connection.CachingConnectionFactory">-->
<!--<constructor-arg ref="remoteJmsFactory"/>-->
<!--<property name="sessionCacheSize" value="100"/>-->
<!--</bean>-->
<!--</property>-->
<!--<property name="explicitQosEnabled" value="true"/>-->
<!--<property name="sessionAcknowledgeModeName" value="CLIENT_ACKNOWLEDGE"/>-->
<!--</bean>-->
<!-- end config to refactor-->
<bean id="distributedWorkerController" class="uk.ac.ebi.interpro.scan.jms.worker.WorkerImpl">
<constructor-arg ref="remoteQueueJmsContainer"/>
<constructor-arg ref="statsMessageListenerJmsContainer"/>
<constructor-arg ref="managerTopicMessageListenerJmsContainer"/>
<property name="maximumIdleTimeSeconds" value="${jvm.maximum.idle.time.seconds}"/>
<property name="maximumLifeSeconds" value="${jvm.maximum.life.seconds}"/>
<property name="highMemory" value="false"/>
<property name="remoteJmsTemplate" ref="remoteJmsTemplate"/>
<property name="localJmsTemplate" ref="inVmJmsTemplate"/>
<property name="remoteWorker" value="true"/>
<property name="statsQueue" ref="statsQueue"/>
<property name="jobRequestQueue" ref="jobRequestQueue" />
<property name="jobResponseQueue" ref="jobResponseQueue" />
<property name="highMemJobRequestQueue" ref="highMemJobRequestQueue"/>
<property name="systemMonitorQueue" ref="monitorQueue"/>
<property name="maxConsumerSize" value="${worker.maxconsumers}" />
<property name="completionFactor" value="20" />
<property name="queueConsumerRatio" value="${steps.to.consumer.ratio}" />
<property name="workerRunner">
<bean class="uk.ac.ebi.interpro.scan.jms.master.queuejumper.platforms.SubmissionWorkerRunner">
<property name="submissionCommand" value="${grid.worker.submit.command} ${worker.command}"/>
<property name="gridCommand" value="${grid.worker.submit.command}"/>
<property name="projectId" value="${user.digest}"/>
<property name="i5Command" value="${worker.command}"/>
<property name="gridJobsLimit" value="${grid.jobs.limit}"/>
<property name="lsfMonitor" ref="lsfMonitor"/>
<property name="highMemory" value="false"/>
<property name="gridName" value="${grid.name}"/>
<property name="workerStartupStrategy">
<bean class="uk.ac.ebi.interpro.scan.jms.master.queuejumper.platforms.UnrestrictedWorkerStartupStrategy"/>
</property>
</bean>
</property>
<property name="temporaryDirectoryManager" ref="tempDirectoryManager"/>
<property name="workerRunnerHighMemory">
<bean class="uk.ac.ebi.interpro.scan.jms.master.queuejumper.platforms.SubmissionWorkerRunner">
<property name="submissionCommand" value="${grid.worker.submit.command} ${worker.high.memory.command}"/>
<property name="gridCommand" value="${grid.worker.submit.high.memory.command}"/>
<property name="projectId" value="${user.digest}"/>
<property name="i5Command" value="${worker.high.memory.command}"/>
<property name="gridJobsLimit" value="${grid.jobs.limit}"/>
<property name="lsfMonitor" ref="lsfMonitor"/>
<property name="gridName" value="${grid.name}"/>
<property name="highMemory" value="true"/>
<property name="workerStartupStrategy">
<bean class="uk.ac.ebi.interpro.scan.jms.master.queuejumper.platforms.UnrestrictedWorkerStartupStrategy"/>
</property>
</bean>
</property>
<property name="statsUtil" ref="workerStatsUtil"/>
<property name="workerManagerTopic" ref="workerManagerTopic"/>
<property name="jmsTopicTemplate" ref="inVmJmsTopicTemplate"/>
<property name="responseQueueMessageListener" ref="responseQueueMessageListener"/>
<property name="workerMonitorQueueListener" ref="monitorQueueMessageListener"/>
<property name="workerMessageSender" ref="workerMessageSender"/>
<property name="gridThrottle" value="${grid.throttle}"/>
<property name="maxUnfinishedJobs" value="${worker.maxunfinished.jobs}"/>
<property name="maxTierDepth" value="${max.tier.depth}"/>
<property name="jmsExceptionListener" ref="workerExceptionListener"/>
<property name="jmsTransportListener" ref="jmsTransportListener"/>
<property name="concurrentInVmWorkerCount" value="${worker.number.of.embedded.workers}"/>
<property name="maxConcurrentInVmWorkerCount" value="${worker.maxnumber.of.embedded.workers}"/>
<property name="gridName" value="${grid.name}"/>
<property name="verboseLog" value="${verbose.log}"/>
<property name="verboseLogLevel" value="${verbose.log.level}"/>
<property name="managerTopicMessageListener" ref="managerTopicMessageListener"/>
<property name="logDir" value="${log.dir}"/>
<property name="workerState" ref="workerState"/>
<property name="timeKeeper" ref="timeKeeper"/>
<property name="gridCheckInterval" value="${grid.check.interval.seconds}"/>
<property name="queuePrefetchLimit" value="${consumer.prefetch.limit}"/>
</bean>
<bean id="portExclusionList" class="java.lang.String">
<constructor-arg value="${tcp.port.exclusion.list}"/>
</bean>
<!-- JMS transport Listener-->
<bean id="jmsTransportListener" class="uk.ac.ebi.interpro.scan.jms.activemq.JMSTransportListener" />
<!-- LSF Monitor-->
<bean id="lsfMonitor" class="uk.ac.ebi.interpro.scan.jms.lsf.LSFMonitor" />
<!--workerState-->
<bean id="workerState" class="uk.ac.ebi.interpro.scan.jms.worker.WorkerState" />
<!--TimeKeeper-->
<bean id="timeKeeper" class="uk.ac.ebi.interpro.scan.jms.worker.TimeKeeper" />
<!--Configuration for the job response queue listener-->
<bean id="responseQueueJmsContainer" class="org.springframework.jms.listener.DefaultMessageListenerContainer">
<property name="connectionFactory" ref="connectionFactory"/>
<property name="destination" ref="jobResponseQueue"/>
<property name="concurrentConsumers" value="1"/>
<property name="messageListener" ref="responseQueueMessageListener"/>
<property name="exceptionListener" ref="workerExceptionListener"/>
</bean>
<!--Listens to the local response queue and propagates to the remote one-->
<bean id="responseQueueMessageListener" class="uk.ac.ebi.interpro.scan.jms.worker.ResponseQueueMessageListener">
<property name="remoteJmsTemplate" ref="remoteJmsTemplate"/>
<property name="jobResponseQueue" ref="jobResponseQueue"/>
<property name="controller" ref="distributedWorkerController"/>
<!--<property name="workerMessageSender" ref="workerMessageSender"/>-->
</bean>
<!--Configuration for the local job queue listener-->
<!--<!–Configuration for the job request queue listener–>-->
<bean id="remoteQueueJmsContainer" depends-on="remoteConnectionFactory" class="org.springframework.jms.listener.DefaultMessageListenerContainer">
<property name="connectionFactory" ref="remoteConnectionFactory" />
<property name="destination" ref="jobRequestQueue"/>
<property name="concurrentConsumers" value="1"/>
<property name="maxConcurrentConsumers" value="1"/>
<property name="sessionTransacted" value="false"/>
<property name="sessionAcknowledgeModeName" value="CLIENT_ACKNOWLEDGE"/>
<property name="receiveTimeout" value="-1"/>
<property name="messageListener" ref="remoteJobQueueListener"/>
<property name="acceptMessagesWhileStopping" value="false"/>
<property name="exceptionListener" ref="workerExceptionListener"/>
<property name="errorHandler" ref="jmsErrorHandler"/>
</bean>
<!--Listens to the remote request queue and propagates to the local one-->
<bean id="remoteJobQueueListener" class="uk.ac.ebi.interpro.scan.jms.worker.RemoteJobQueueListener">
<property name="localJmsTemplate" ref="inVmJmsTemplate"/>
<property name="jobRequestQueue" ref="jobRequestQueue"/>
<property name="workerMessageSender" ref="workerMessageSender"/>
<property name="statsUtil" ref="workerStatsUtil"/>
<property name="gridThrottle" value="${grid.throttle}"/>
<property name="maxUnfinishedJobs" value="${worker.maxunfinished.jobs}"/>
<property name="workerState" ref="workerState"/>
</bean>
<bean id="localQueueJmsContainer" class="org.springframework.jms.listener.DefaultMessageListenerContainer">
<property name="connectionFactory" ref="connectionFactory"/>
<property name="destination" ref="jobRequestQueue"/>
<property name="messageListener" ref="localJobQueueListener"/>
<property name="concurrentConsumers" value="${worker.number.of.embedded.workers}"/>
<property name="maxConcurrentConsumers" value="${worker.maxnumber.of.embedded.workers}"/>
<property name="sessionTransacted" value="true"/>
<property name="sessionAcknowledgeModeName" value="CLIENT_ACKNOWLEDGE"/>
<property name="exceptionListener" ref="workerExceptionListener"/>
</bean>
<!--Listens to the local job queue and performs jobs-->
<bean id="localJobQueueListener" class="uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener">
<property name="stepExecutor" ref="embeddedStepExecutor"/>
<property name="jobResponseQueue" ref="jobResponseQueue"/>
<property name="localJmsTemplate" ref="inVmJmsTemplate"/>
<property name="controller" ref="distributedWorkerController"/>
<property name="verboseLog" value="${verbose.log}"/>
<property name="statsUtil" ref="workerStatsUtil"/>
</bean>
<!--<bean id="localJobQueueListener" class="uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener">-->
<!--<property name="jobResponseQueue" ref="jobResponseQueue"/>-->
<!--<property name="jmsTemplate" ref="localJmsTemplate"/>-->
<!--<property name="stepExecutor" ref="embeddedStepExecutor"/>-->
<!--</bean>-->
<bean id="embeddedStepExecutor" class="uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl">
<property name="jobs" ref="jobs"/>
<property name="jmsTemplate" ref="inVmJmsTemplate"/>
<property name="jobResponseQueue" ref="jobResponseQueue"/>
<property name="directoryManager" ref="tempDirectoryManager"/>
</bean>
<!--Configuration for the statistics listener-->
<bean id="statsMessageListenerJmsContainer" class="org.springframework.jms.listener.DefaultMessageListenerContainer">
<property name="connectionFactory" ref="connectionFactory"/>
<property name="destination" ref="statsQueue"/>
<property name="concurrentConsumers" value="1"/>
<property name="messageListener" ref="statsMessageListener"/>
</bean>
<bean id="statsMessageListener" class="uk.ac.ebi.interpro.scan.jms.stats.StatsMessageListener"/>
<!--Configuration for the topic listener-->
<bean id="managerTopicMessageListenerJmsContainer" class="org.springframework.jms.listener.DefaultMessageListenerContainer">
<property name="connectionFactory" ref="connectionFactory"/>
<property name="destination" ref="workerManagerTopic"/>
<property name="messageListener" ref="managerTopicMessageListener"/>
<property name="pubSubDomain" value="true" />
<property name="errorHandler" ref="jmsErrorHandler"/>
</bean>
<bean id="managerTopicMessageListener" class="uk.ac.ebi.interpro.scan.jms.worker.ManagerTopicMessageListener">
<property name="workerMessageSender" ref="workerMessageSender"/>
</bean>
<!-- The worker Sender Implementation used by listeners-->
<bean id="workerMessageSender" class="uk.ac.ebi.interpro.scan.jms.worker.WorkerMessageSenderImpl">
<property name="localJmsTemplate" ref="inVmJmsTemplate"/>
<property name="remoteJmsTemplate" ref="remoteJmsTemplate"/>
<property name="jmsTopicTemplate" ref="inVmJmsTopicTemplate"/>
<property name="workerJobRequestQueue" ref="jobRequestQueue"/>
<property name="workerManagerTopic" ref="workerManagerTopic"/>
<property name="highmemWorkerJobRequestQueue" ref="highMemJobRequestQueue"/>
</bean>
<!--Listens to the local response queue and propagates to the remote one-->
<bean id="monitorQueueMessageListener" class="uk.ac.ebi.interpro.scan.jms.monitoring.WorkerMonitorQueueListener">
<property name="remoteJmsTemplate" ref="remoteJmsTemplate"/>
<property name="systemMonitorQueue" ref="monitorQueue"/>
<!--<property name="workerMessageSender" ref="workerMessageSender"/>-->
</bean>
<bean id="workerStatsUtil" class="uk.ac.ebi.interpro.scan.jms.stats.StatsUtil">
<property name="jmsTemplate" ref="inVmJmsTemplate"/>
<property name="jobRequestQueue" ref="jobRequestQueue"/>
<property name="jobResponseQueue" ref="jobResponseQueue"/>
<property name="workerManagerTopicQueue" ref="workerManagerTopic"/>
<property name="statsQueue" ref="statsQueue"/>
<property name="statsMessageListener" ref="statsMessageListener" />
<property name="highMemJobRequestQueue" ref="highMemJobRequestQueue"/>
<property name="totalJobs" value="0"/>
<property name="unfinishedJobs" value="0"/>
</bean>
<bean id="tempDirectoryManager" class="uk.ac.ebi.interpro.scan.io.ExternallySetLocationTemporaryDirectoryManager"/>
</beans>
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