server-webapp/src/main/webapp/WEB-INF/beans.xml

<?xml version="1.0" encoding="UTF-8"?>
<!-- Copyright (C) 2010-2011 The University of Manchester See the file "LICENSE" 
	for license terms. -->
<beans xmlns="http://www.springframework.org/schema/beans"
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:context="http://www.springframework.org/schema/context"
	xmlns:task="http://www.springframework.org/schema/task" xmlns:util="http://www.springframework.org/schema/util"
	default-lazy-init="false"
	xsi:schemaLocation="http://www.springframework.org/schema/task http://www.springframework.org/schema/task/spring-task-3.0.xsd
		http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
		http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util-3.0.xsd
		http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-3.0.xsd">

	<bean id="webapp" class="org.taverna.server.master.TavernaServer">
		<property name="policy" ref="worker.policy" />
		<property name="runStore" ref="worker.rundb" />
		<property name="fileUtils" ref="fileUtils" />
		<property name="contentsDescriptorBuilder" ref="contentsDescriptorBuilder" />
		<property name="notificationEngine" ref="notificationFabric" />
		<property name="support" ref="webapp.support" />
		<property name="eventSource" ref="dispatch.atom" />
		<property name="interactionFeed" value="${taverna.interaction.feed_path}" />
		<lookup-method name="makeRunInterface" bean="run.coreView.prototype" />
		<lookup-method name="getPolicyDescription" bean="webapp.policyView" />
	</bean>

	<bean id="webapp.support" class="org.taverna.server.master.TavernaServerSupport">
		<property name="policy" ref="worker.policy" />
		<property name="listenerFactory" ref="localworker.factory" />
		<property name="runFactory" ref="localworker.factory" />
		<property name="fileUtils" ref="fileUtils" />
		<property name="runStore" ref="worker.rundb" />
		<property name="stateModel" ref="webapp.state" />
		<property name="idMapper" ref="IdentityMapper" />
		<property name="invocationCounter" ref="webapp.invocationCounter" />
		<property name="webapp" ref="webapp" />
		<property name="contentTypeMap">
			<map key-type="java.lang.String" value-type="java.lang.String">
				<description>Maps suffixes (post '.') to content types.</description>
				<entry key="baclava" value="application/vnd.taverna.baclava+xml" />
				<entry key="robundle.zip" value="application/vnd.wf4ever.robundle+zip" />
			</map>
		</property>
		<property name="capabilitySource" ref="capabilities" />
	</bean>

	<bean id="capabilities" class="org.taverna.server.master.utils.CapabilityLister" />

	<bean id="webapp.policyView" class="org.taverna.server.master.PolicyREST">
		<property name="support" ref="webapp.support" />
		<property name="policy" ref="worker.policy" />
		<property name="listenerFactory" ref="localworker.factory" />
		<property name="notificationEngine" ref="notificationFabric" />
	</bean>

	<bean id="contentsDescriptorBuilder" class="org.taverna.server.master.ContentsDescriptorBuilder">
		<property name="uriBuilderFactory" ref="webapp" />
		<property name="fileUtils" ref="fileUtils" />
	</bean>

	<bean id="webapp.state" class="org.taverna.server.master.ManagementState">
		<description>The initial state of the webapp.</description>
		<property name="logIncomingWorkflows" value="${default.logworkflows}" />
		<property name="allowNewWorkflowRuns" value="${default.permitsubmit}" />
		<property name="logOutgoingExceptions" value="${default.logexceptions}" />
		<property name="persistenceManagerBuilder" ref="pmb" />
		<property name="self" ref="webapp.state" />
	</bean>

	<bean id="webapp.invocationCounter" class="org.taverna.server.master.utils.InvocationCounter" />
	<bean id="webapp.perfLogger" class="org.taverna.server.master.utils.CallTimeLogger">
		<property name="threshold" value="${calltime.logthreshold:4000000}" />
	</bean>

	<bean id="run.coreView.prototype" scope="prototype"
		class="org.taverna.server.master.RunREST">
		<property name="support" ref="webapp.support" />
		<property name="cdBuilder" ref="contentsDescriptorBuilder" />
		<lookup-method name="makeSecurityInterface" bean="run.securityView.prototype" />
		<lookup-method name="makeInputInterface" bean="run.inputView.prototype" />
		<lookup-method name="makeListenersInterface" bean="run.listenersView.prototype" />
		<lookup-method name="makeDirectoryInterface" bean="run.directoryView.prototype" />
		<lookup-method name="makeInteractionFeed" bean="run.interactionFeed.prototype" />
	</bean>

	<bean id="run.directoryView.prototype" scope="prototype"
		class="org.taverna.server.master.DirectoryREST">
		<property name="support" ref="webapp.support" />
		<property name="fileUtils" ref="fileUtils" />
	</bean>

	<bean id="run.listenersView.prototype" scope="prototype"
		class="org.taverna.server.master.ListenersREST">
		<property name="support" ref="webapp.support" />
		<lookup-method name="makeListenerInterface" bean="run.singleListenerView.prototype" />
	</bean>

	<bean id="run.singleListenerView.prototype" scope="prototype"
		class="org.taverna.server.master.SingleListenerREST">
		<lookup-method name="makePropertyInterface" bean="run.propertyView.prototype" />
	</bean>

	<bean id="run.propertyView.prototype" scope="prototype"
		class="org.taverna.server.master.ListenerPropertyREST">
		<property name="support" ref="webapp.support" />
	</bean>

	<bean id="run.inputView.prototype" scope="prototype"
		class="org.taverna.server.master.InputREST">
		<property name="support" ref="webapp.support" />
		<property name="cdBuilder" ref="contentsDescriptorBuilder" />
		<property name="fileUtils" ref="fileUtils" />
	</bean>

	<bean id="run.securityView.prototype" scope="prototype"
		class="org.taverna.server.master.RunSecurityREST">
		<property name="support" ref="webapp.support" />
	</bean>

	<bean id="run.interactionFeed.prototype" scope="prototype"
		class="org.taverna.server.master.InteractionFeed">
		<property name="interactionFeedSupport" ref="interactionFeed" />
	</bean>

	<bean id="feed" class="org.taverna.server.master.notification.atom.AtomFeed">
		<property name="eventSource" ref="dispatch.atom" />
		<property name="support" ref="webapp.support" />
		<property name="feedLanguage" value="${atom.language}" />
		<property name="abdera" ref="abdera" />
	</bean>

	<bean id="admin" class="org.taverna.server.master.admin.AdminBean">
		<property name="adminHtmlFile" value="/admin.html" />
		<property name="counter" ref="webapp.invocationCounter" />
		<property name="factory" ref="localworker.factory" />
		<property name="localWorkerModel" ref="localworker.state" />
		<property name="runDB" ref="worker.rundb" />
		<property name="state" ref="webapp.state" />
		<property name="usageRecords" ref="usageRecordSink" />
		<property name="userStore" ref="userStore" />
	</bean>

	<bean id="IdentityMapper" class="org.taverna.server.master.identity.CompositeIDMapper">
		<property name="identityMappers">
			<list>
				<bean id="AuthorityBased"
					class="org.taverna.server.master.identity.AuthorityDerivedIDMapper">
					<description>Derives the local user identity to use for execution
						from the LOCALUSER_* Spring Security authority. Thus, if the user
						has &quot;LOCALUSER_foo&quot;, they will be executing as the local
						user id &quot;foo&quot;.</description>
				</bean>
				<bean id="SelfAccess"
					class="org.taverna.server.master.identity.WorkflowInternalAuthProvider.WorkflowSelfIDMapper">
					<description>Handles the case where a workflow is accessing itself for
						the purpose of publishing interactions.</description>
					<property name="runStore" ref="worker.rundb" />
				</bean>
				<bean id="Extracting" class="org.taverna.server.master.identity.NameIDMapper">
					<description>An alternate mechanism for mapping users. This tries
						to use an RE to extract the user name from the principal name.
					</description>
					<property name="regexp" value="${localusernameregexp}">
						<description>An optional regexp to extract the local user name
							from the principal's string description. The first capturing
							group will be the result of the mapping operation.
						</description>
					</property>
				</bean>
				<bean id="Constant" class="org.taverna.server.master.identity.ConstantIDMapper">
					<description>How to map web principals to local users. This one
						maps everyone to the same user, "taverna".
					</description>
					<property name="constantId" value="${default.localusername}" />
				</bean>
			</list>
		</property>
	</bean>

	<bean id="passwordEncoder"
		class="org.springframework.security.crypto.bcrypt.BCryptPasswordEncoder" />
	<bean class="org.taverna.server.master.identity.UserStore" id="userStore">
		<property name="persistenceManagerBuilder" ref="pmb" />
		<property name="baselineUserProperties">
			<util:properties location="/WEB-INF/security/users.properties" />
		</property>
		<property name="defaultLocalUser" value="${default.localusername}" />
		<property name="encoder" ref="passwordEncoder" />
	</bean>

	<!-- <bean id="sessionFactory" class="org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean"> 
		<property name="dataSource" ref="dataSource" /> <property name="hibernateProperties"> 
		<props> <prop key="hibernate.dialect">org.hibernate.dialect.DerbyDialect</prop> 
		<prop key="hibernate.hbm2ddl.auto">create</prop> </props> </property> <property 
		name="annotatedClasses"> <list> </list> </property> </bean> -->
	<bean id="pmb" class="org.taverna.server.master.utils.JDOSupport.PersistenceManagerBuilder">
		<property name="persistenceManagerFactory">
			<bean id="pmf" class="org.datanucleus.api.jdo.JDOPersistenceManagerFactory"
				destroy-method="close">
				<property name="connectionFactory" ref="dataSource" />
				<property name="nontransactionalRead" value="true" />
				<property name="persistenceProperties">
					<props>
						<prop key="datanucleus.storeManagerType">rdbms</prop>
						<prop key="datanucleus.autoCreateTables">true</prop>
						<prop key="datanucleus.autoCreateTables">true</prop>
						<prop key="datanucleus.validateTables">true</prop>
						<prop key="datanucleus.autoCreateColumns">true</prop>
						<prop key="datanucleus.autoCreateConstraints">true</prop>
						<prop key="datanucleus.validateConstraints">true</prop>
						<prop key="datanucleus.autoCreateSchema">true</prop>
						<prop key="datanucleus.PersistenceUnitName">TavernaServer</prop>
						<prop key="datanucleus.rdbms.datastoreAdapterClassName"
							>org.taverna.server.master.utils.LoggingDerbyAdapter</prop>
					</props>
				</property>
			</bean>
		</property>
	</bean>
	<bean id="transactionAspect"
		class="org.taverna.server.master.utils.JDOSupport.TransactionAspect" />

	<bean id="systemPrereqs" class="org.springframework.beans.factory.config.MethodInvokingFactoryBean">
		<description>http://stackoverflow.com/questions/3339736/set-system-property-with-spring-configuration-file</description>
		<property name="targetObject" value="#{@systemProperties}" />
		<property name="targetMethod" value="putAll" />
		<property name="arguments">
			<util:properties>
				<prop key="derby.stream.error.field">org.taverna.server.master.utils.DerbyUtils.TO_LOG</prop>
				<prop key="derby.stream.error.logSeverityLevel">30000</prop>
			</util:properties>
		</property>
	</bean>
	<!-- TODO: control the location of the database properly, or move to JNDI 
		TODO: review whether what we are doing now is correct! -->
	<bean id="dataSource" class="org.taverna.server.master.utils.WebappAwareDataSource">
		<property name="driverClassName" value="org.apache.derby.jdbc.EmbeddedDriver" />
		<property name="url"
			value="jdbc:derby:directory:%{WEBAPPROOT}tavernaserver;create=true" />
		<!-- Needed for Derby... -->
		<property name="shutdownUrl"
			value="jdbc:derby:directory:%{WEBAPPROOT}tavernaserver;shutdown=true" />
		<property name="username" value="taverna" />
		<property name="password" value="" />
		<property name="contextualizer" ref="contextualizer" />
	</bean>

	<bean id="contextualizer" class="org.taverna.server.master.utils.Contextualizer" />

	<bean id="usageRecordSink" class="org.taverna.server.master.usage.UsageRecordRecorder">
		<property name="state" ref="webapp.state" />
		<property name="contextualizer" ref="contextualizer" />
		<property name="persistenceManagerBuilder" ref="pmb" />
		<property name="self" ref="usageRecordSink" />
		<property name="disableDB" value="${usage.disableDB}" />
		<property name="logFile" value="${usage.logFile}" />
	</bean>

	<context:property-placeholder
		ignore-unresolvable="true" order="2" properties-ref="default-factory-properties" />
	<util:properties id="default-factory-properties">
		<prop key="backEndFactory">org.taverna.server.master.localworker.IdAwareForkRunFactory</prop>
	</util:properties>

	<!-- This bean configuration replaced with org.taverna.server.master.localworker.LocalWorkerFactory -->
	<!-- <bean id="localworker.factory" scope="singleton" lazy-init="false" 
		class="${backEndFactory}"> <description> The simple policy manager and factory 
		for the baseline localworker case. </description> <property name="state" 
		ref="localworker.state" /> <property name="runDB" ref="worker.rundb" 
		/> -->
	<!-- Handled by autowiring to make type-resilient. -->
	<!-- <property name="idMapper" ref="IdentityMapper" /> -->
	<!-- <property name="securityContextFactory" ref="worker.securityContext" 
		/> <property name="usageRecordSink" ref="usageRecordSink" /> <property name="URProcessorPool" 
		ref="URThreads" /> </bean> -->

	<!-- <task:executor id="URThreads" pool-size="${pool.size}" /> -->

	<bean id="worker.securityContext"
		class="org.taverna.server.master.worker.SecurityContextFactory">
		<property name="runDatabase" ref="worker.rundb" />
		<property name="filenameConverter" ref="fileUtils" />
		<property name="x500Utils" ref="x500Utils" />
		<property name="httpRealm" value="${http.realmName}" />
		<property name="uriSource" ref="webapp" />
		<property name="certificateFetcher" ref="certificateChainFetcher" />
		<property name="passwordIssuer" ref="passwordIssuer" />
	</bean>

	<bean id="passwordIssuer" class="org.taverna.server.master.worker.PasswordIssuer">
		<!-- <property name="length" value="8" /> -->
	</bean>

	<bean id="certificateChainFetcher" class="org.taverna.server.master.utils.CertificateChainFetcher">
		<property name="secure" value="${fetchCertificateChain}" />
	</bean>

	<bean id="localworker.state" class="org.taverna.server.master.localworker.LocalWorkerState"
		scope="singleton" lazy-init="false">
		<description>
			The state of the simple factory for the identity-aware
			local worker.
		</description>
		<property name="defaultLifetime" value="${default.lifetime}">
			<description>How long the run lasts for by default, in seconds.
			</description>
		</property>
		<property name="maxRuns" value="${default.runlimit}">
			<description>The maximum simultaneous number of runs.</description>
		</property>
		<property name="operatingLimit" value="${default.operatinglimit}">
			<description>
				The maximum number of runs that are in the Operating state,
				i.e., actually running with a process consuming resources.
			</description>
		</property>
		<property name="extraArgs">
			<description>Any extra arguments (memory control, etc.) to pass to
				the spawned subprocesses.
			</description>
			<list>
			</list>
		</property>
		<property name="waitSeconds" value="40">
			<description>An upper bound (in seconds) on the time to wait for a
				subprocess to start before failing it.
			</description>
		</property>
		<property name="sleepMS" value="1000">
			<description>The time to wait (in milliseconds) between polling for
				the subprocess to complete its registration.
			</description>
		</property>
		<property name="persistenceManagerBuilder" ref="pmb" />
		<!-- <property name="javaBinary"> <description>The name of the java executable 
			used to run the server worker. Defaults to the executable used to run the 
			hosting environment.</description> </property> -->
		<!-- <property name="serverWorkerJar"> <description>The full path to the 
			executable JAR file containing the implementation of the server worker.</description> 
			</property> -->
		<!-- <property name="executeWorkflowScript"> <description>The full path 
			to the executeworkflow.sh in either the Taverna 2 Workbench distribution 
			or the Taverna 2 Command Line distribution.</description> </property> -->
		<property name="self" ref="localworker.state" />
		<property name="defaultExecuteWorkflowScript" value="${executeWorkflowScript:NONE}" />
	</bean>

	<bean id="worker.policy" class="org.taverna.server.master.worker.PolicyImpl">
		<description>
			The implementation of the access control policy supported
			by the localworker run engine.
		</description>
		<property name="limits" ref="localworker.state" />
		<property name="runDB" ref="worker.rundb" />
	</bean>
	<bean id="worker.rundb" class="org.taverna.server.master.worker.RunDatabase">
		<property name="notifier" ref="worker.notifier" />
		<property name="typeNotifiers">
			<list>
				<ref bean="cn.email" />
				<ref bean="cn.sms" />
				<ref bean="cn.twitter" />
				<!-- <ref bean="cn.xmpp"/> -->
			</list>
		</property>
		<property name="notificationEngine" ref="notificationFabric" />
		<property name="dao" ref="worker.runDAO" />
	</bean>
	<bean id="cn.email"
		class="org.taverna.server.master.worker.VelocityCompletionNotifier">
		<property name="name" value="email" />
		<property name="subject" value="Workflow run finished executing" />
		<property name="velocityEngine" ref="velocity" />
		<property name="uriBuilderFactory" ref="webapp" />
	</bean>
	<bean id="cn.sms"
		class="org.taverna.server.master.worker.VelocityCompletionNotifier">
		<property name="name" value="sms" />
		<property name="subject" value="Run finished" />
		<property name="velocityEngine" ref="velocity" />
		<property name="uriBuilderFactory" ref="webapp" />
	</bean>
	<bean id="cn.twitter"
		class="org.taverna.server.master.worker.VelocityCompletionNotifier">
		<property name="name" value="twitter" />
		<property name="subject" value="Run finished" />
		<property name="velocityEngine" ref="velocity" />
		<property name="uriBuilderFactory" ref="webapp" />
	</bean>
	
	<bean id="worker.runDAO" class="org.taverna.server.master.worker.RunDatabaseDAO">
		<description>
			The implementation of the catalog of workflow runs
			supported by the localworker run engine.
		</description>
		<property name="persistenceManagerBuilder" ref="pmb" />
		<property name="facade" ref="worker.rundb" />
	</bean>
	<task:scheduled-tasks scheduler="taskScheduler">
		<task:scheduled ref="worker.rundb" method="cleanNow"
			fixed-delay="${purge.interval}" />
		<task:scheduled ref="worker.rundb" method="checkForFinishNow"
			fixed-delay="${finish.interval}" />
		<task:scheduled ref="dispatch.atom" method="deleteExpiredEvents"
			fixed-delay="${atom.cleaninterval}" />
	</task:scheduled-tasks>

	<bean id="notificationFabric"
		class="org.taverna.server.master.notification.NotificationEngine">
		<property name="dispatchers">
			<list>
				<ref bean="dispatch.email" />
				<ref bean="dispatch.twitter" />
				<ref bean="dispatch.xmpp" />
				<ref bean="dispatch.sms" />
			</list>
		</property>
		<property name="universalDispatchers">
			<list>
				<ref bean="dispatch.atom" />
			</list>
		</property>
	</bean>

	<bean id="dispatch.email" class="org.taverna.server.master.notification.EmailDispatcher">
		<property name="from" value="${email.from}" />
		<property name="messageContentType" value="${email.type}" />
		<property name="cooldownSeconds" value="${message.cooldown}" />
		<property name="smtpHost" value="${email.host}" />
		<property name="sender">
			<bean class="org.springframework.mail.javamail.JavaMailSenderImpl"
				id="javamail">
				<property name="host" value="${email.host}" />
			</bean>
		</property>
	</bean>
	<bean id="dispatch.twitter"
		class="org.taverna.server.master.notification.TwitterDispatcher">
		<property name="cooldownSeconds" value="${message.cooldown}" />
		<property name="accessToken" value="${twitter.oauth.accessToken}" />
		<property name="accessSecret" value="${twitter.oauth.accessTokenSecret}" />
	</bean>
	<bean id="dispatch.xmpp" class="org.taverna.server.master.notification.JabberDispatcher">
		<property name="resource" value="${xmpp.resource}" />
		<property name="host" value="${xmpp.service}" />
		<property name="username" value="${xmpp.user}" />
		<property name="password" value="${xmpp.password}" />
	</bean>
	<bean id="dispatch.sms" class="org.taverna.server.master.notification.SMSDispatcher">
		<property name="usernameField" value="${sms.userfield}" />
		<property name="passwordField" value="${sms.passfield}" />
		<property name="destinationField" value="${sms.destfield}" />
		<property name="messageField" value="${sms.msgfield}" />
		<property name="cooldownSeconds" value="${message.cooldown}" />
	</bean>

	<bean id="dispatch.atom" class="org.taverna.server.master.notification.atom.EventDAO">
		<property name="expiryAgeDays" value="${atom.lifespan}" />
		<property name="persistenceManagerBuilder" ref="pmb" />
		<property name="uriBuilderFactory" ref="feed" />
		<property name="self" ref="dispatch.atom" />
	</bean>

	<bean id="worker.notifier"
		class="org.taverna.server.master.worker.SimpleFormattedCompletionNotifier">
		<property name="subject" value="${message.termination.subject}" />
		<property name="messageFormat" value="${message.termination.body}" />
		<property name="name" value="fallback"/>
	</bean>

	<bean id="fileUtils" class="org.taverna.server.master.utils.FilenameUtils" />
	<bean id="x500Utils" class="org.taverna.server.master.utils.X500Utils" />
	<task:scheduler id="taskScheduler" pool-size="${pool.size}" />

	<bean class="org.taverna.server.master.utils.JCECheck" id="JCECheck" />

	<bean class="org.taverna.server.master.interaction.InteractionFeedSupport"
		id="interactionFeed" scope="singleton">
		<property name="abdera" ref="abdera" />
		<property name="support" ref="webapp.support" />
		<property name="uriBuilder" ref="webapp" />
		<property name="utils" ref="fileUtils" />
	</bean>
	<bean class="org.taverna.server.master.rest.handler.FeedHandler" id="atomFeedHandler">
		<property name="abdera" ref="abdera" />
	</bean>
	<bean class="org.taverna.server.master.rest.handler.EntryHandler" id="atomEntryHandler">
		<property name="abdera" ref="abdera" />
	</bean>

	<bean id="authProvider" class="org.taverna.server.master.identity.StrippedDownAuthProvider">
		<property name="passwordEncoder" ref="passwordEncoder" />
		<property name="userDetailsService">
			<bean class="org.taverna.server.master.identity.UserStore.CachedUserStore">
				<property name="realStore" ref="userStore" />
			</bean>
		</property>
	</bean>
	<bean id="workflowInternalAuthProvder"
		class="org.taverna.server.master.identity.WorkflowInternalAuthProvider">
		<property name="dao" ref="worker.runDAO" />
		<property name="cacheBound" value="${default.runlimit}" />
	</bean>
	<bean id="velocity" class="org.apache.velocity.app.VelocityEngine"
		init-method="init" lazy-init="false">
		<constructor-arg>
			<props>
				<prop key="input.encoding">UTF-8</prop>
				<prop key="output.encoding">UTF-8</prop>
				<prop key="runtime.log.logsystem.class">org.apache.velocity.runtime.log.Log4JLogChute</prop>
				<prop key="runtime.log.logsystem.log4j.logger">org.taverna.server.master.worker.VelocityCompletionNotifier</prop>
				<prop key="resource.loader">class</prop>
				<prop key="class.resource.loader.description">Velocity Classpath Resource Loader</prop>
				<prop key="class.resource.loader.class">org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader</prop>
			</props>
		</constructor-arg>
	</bean>
	<bean id="abdera" class="org.apache.abdera.Abdera"/>
</beans>