Could not resolve placeholder 'fcrepo.modeshape.configuration' Tomcat8 | CentOS

[Devin Griffin]

I'm trying to install the latest version of Fedora on Tomcat 8 on top of CentOS.

It's giving me this error:

HTTP Status 500 - Servlet.init() for servlet jersey-servlet threw exception

type Exception report

message Servlet.init() for servlet jersey-servlet threw exception

description The server encountered an internal error that prevented it from fulfilling this request.

exception

javax.servlet.ServletException: Servlet.init() for servlet jersey-servlet threw exception
	org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504)
	org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
	org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
	org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
	org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1132)
	org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
	org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
	org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	java.lang.Thread.run(Thread.java:748)

root cause

org.springframework.beans.factory.BeanDefinitionStoreException: Invalid bean definition with name 'modeshapeRepofactory' defined in class path resource [spring/repo.xml]: Could not resolve placeholder 'fcrepo.modeshape.configuration' in string value "${fcrepo.modeshape.configuration}"; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'fcrepo.modeshape.configuration' in string value "${fcrepo.modeshape.configuration}"
	org.springframework.beans.factory.config.PlaceholderConfigurerSupport.doProcessProperties(PlaceholderConfigurerSupport.java:223)
	org.springframework.beans.factory.config.PropertyPlaceholderConfigurer.processProperties(PropertyPlaceholderConfigurer.java:222)
	org.springframework.beans.factory.config.PropertyResourceConfigurer.postProcessBeanFactory(PropertyResourceConfigurer.java:86)
	org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:284)
	org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:166)
	org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:681)
	org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:523)
	org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:444)
	org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:326)
	org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
	org.fcrepo.http.commons.FedoraContextLoaderListener.contextInitialized(FedoraContextLoaderListener.java:40)
	org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
	org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:976)
	org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1853)
	java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	java.util.concurrent.FutureTask.run(FutureTask.java:266)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	java.lang.Thread.run(Thread.java:748)

root cause

java.lang.IllegalArgumentException: Could not resolve placeholder 'fcrepo.modeshape.configuration' in string value "${fcrepo.modeshape.configuration}"
	org.springframework.util.PropertyPlaceholderHelper.parseStringValue(PropertyPlaceholderHelper.java:174)
	org.springframework.util.PropertyPlaceholderHelper.replacePlaceholders(PropertyPlaceholderHelper.java:126)
	org.springframework.beans.factory.config.PropertyPlaceholderConfigurer$PlaceholderResolvingStringValueResolver.resolveStringValue(PropertyPlaceholderConfigurer.java:258)
	org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveStringValue(BeanDefinitionVisitor.java:282)
	org.springframework.beans.factory.config.BeanDefinitionVisitor.resolveValue(BeanDefinitionVisitor.java:209)
	org.springframework.beans.factory.config.BeanDefinitionVisitor.visitPropertyValues(BeanDefinitionVisitor.java:141)
	org.springframework.beans.factory.config.BeanDefinitionVisitor.visitBeanDefinition(BeanDefinitionVisitor.java:82)
	org.springframework.beans.factory.config.PlaceholderConfigurerSupport.doProcessProperties(PlaceholderConfigurerSupport.java:220)
	org.springframework.beans.factory.config.PropertyPlaceholderConfigurer.processProperties(PropertyPlaceholderConfigurer.java:222)
	org.springframework.beans.factory.config.PropertyResourceConfigurer.postProcessBeanFactory(PropertyResourceConfigurer.java:86)
	org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:284)
	org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:166)
	org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:681)
	org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:523)
	org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:444)
	org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:326)
	org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
	org.fcrepo.http.commons.FedoraContextLoaderListener.contextInitialized(FedoraContextLoaderListener.java:40)
	org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
	org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:976)
	org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1853)
	java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	java.util.concurrent.FutureTask.run(FutureTask.java:266)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	java.lang.Thread.run(Thread.java:748)

note The full stack trace of the root cause is available in the Apache Tomcat/8.0.47 logs.

---

Apache Tomcat/8.0.47

After some Google searches, I believe the issue is this:

JAVA_OPTS="${JAVA_OPTS} -Dfcrepo.modeshape.configuration=classpath:/config/file-simple/repository.json -Dfcrepo.home=/mnt/fedora-data"

However, I have tried to get that system property configured every way I've seen online with no resolve.

Where do I put the JAVA_OPTS statement on CentOS w/Tomcat8?



[Bethany Seeger]

Hi Devin, 

I have fedora install on a CentOS server where I have tomcat8 located in /var/tomcat (essentially, I followed these instructions, though I chose to put it in a different spot: https://www.digitalocean.com/community/tutorials/how-to-install-apache-tomcat-8-on-centos-7).

Tomcat has a file in the /etc/systemd/system/ folder named tomcat.service with the following environment information:

(note that I have it refer to files I store in /etc/fedora — like the repository.json, activemq.xml, audit.xml file – your statements will vary) 

----------

Environment=JAVA_HOME=/usr/lib/jvm/jre

Environment=CATALINA_PID=/var/tomcat/temp/tomcat.pid

Environment=CATALINA_HOME=/var/tomcat

Environment=CATALINA_BASE=/var/tomcat

#Environment='CATALINA_OPTS=-Xms512M -Xmx1024M -server -XX:+UseParallelGC'

Environment='CATALINA_OPTS=-Xms512M -Xmx1024M -server -Dcantaloupe.config=/opt/cantaloupe/cantaloupe.properties'

Environment='JAVA_OPTS=-Djava.awt.headless=true -Dfile.encoding=UTF-8 -server -Dfcrepo.modeshape.configuration=file:/etc/fcrepo/repository.json -Dfcrepo.home=/opt/fcrepo/fcrepo4-data -Dfcrepo.binary.directory=binary.store -Dfcrepo.activemq.configuration=file:/etc/fcrepo/activemq.xml -Dfcrepo.activemq.directory=activemq -Dfcrepo.modeshape.index.directory=modeshape.index -Dfcrepo.audit.container=/audit -Dcom.arjuna.ats.arjuna.common.ObjectStoreEnvironmentBean.default.objectStoreDir=arjuna.common.object.store -Dcom.arjuna.ats.arjuna.objectstore.objectStoreDir=arjuna.object.store -Dnet.sf.ehcache.skipUpdateCheck=true -Xms1024m -Xmx2048m -XX:NewSize=256m -XX:MaxNewSize=256m -XX:MaxMetaspaceSize=512M -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled -XX:ConcGCThreads=5 -XX:MaxGCPauseMillis=200 -XX:ParallelGCThreads=20 -Dfcrepo.spring.audit.configuration=file:/etc/fcrepo/audit.xml -Dlogback.configurationFile=/etc/fcrepo/logback.xml

I can stop/start/restart tomcat via:

$> systemctl stop tomcat

Hope that helps some. 

Bethany

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[Devin Griffin]

Thank you!

I changed my tomcat.service to:

Description=Apache Tomcat Web Application Container
After=syslog.target network.target

[Service]
Type=forking

Environment=JAVA_HOME=/usr/lib/jvm/jre
Environment=CATALINA_PID=/opt/tomcat/temp/tomcat.pid
Environment=CATALINA_HOME=/opt/tomcat
Environment=CATALINA_BASE=/opt/tomcat

Environment='CATALINA_OPTS=-Xms512M -Xmx1024M -server -XX:+UseParallelGC'

Environment='JAVA_OPTS=-Djava.awt.headless=true -Djava.security.egd=file:/dev/./urandom -Dfcrepo.modeshape.configuration=classpath:/config/file-simple/repository.json -Dfcrepo.home=/mnt/fedora-data'

ExecStart=/opt/tomcat/bin/startup.sh
ExecStop=/bin/kill -15 $MAINPID

User=tomcat
Group=tomcat

[Install]
WantedBy=multi-user.target

Now, I get this error:

HTTP Status 404 - /fcrepo-webapp-4.7.4/

type Status report

message /fcrepo-webapp-4.7.4/

description The requested resource is not available.

---

Apache Tomcat/8.0.47

 
I made sure that the fedora-data file is actually there and that the repository.json path is correct.

[Bethany Seeger]

Hi Devin, 

Can you share your tomcat log?  I’d be curious to see the startup information up through this error message.  

Thanks,

[Devin Griffin]

Is this the correct log file?

07-Nov-2017 16:11:44.493 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log No Spring WebApplicationInitializer types detected on classpath
07-Nov-2017 16:11:47.708 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
07-Nov-2017 16:12:23.681 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log 1 Spring WebApplicationInitializers detected on classpath
07-Nov-2017 16:12:24.577 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
07-Nov-2017 16:12:30.043 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.fcrepo.http.commons.FedoraContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'modeshapeRepofactory': Invocation of init method failed; nested exception is org.fcrepo.kernel.api.exception.RepositoryRuntimeException: java.lang.IllegalStateException: This store is read-only [1.4.191/2]
    at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:136)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:408)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1575)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:732)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:861)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:541)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:444)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:326)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.fcrepo.http.commons.FedoraContextLoaderListener.contextInitialized(FedoraContextLoaderListener.java:40)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4853)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5314)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:753)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:729)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:976)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1853)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.fcrepo.kernel.api.exception.RepositoryRuntimeException: java.lang.IllegalStateException: This store is read-only [1.4.191/2]
    at org.fcrepo.kernel.modeshape.spring.ModeShapeRepositoryFactoryBean.buildRepository(ModeShapeRepositoryFactoryBean.java:86)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:365)
    at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:310)
    at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:133)
    ... 28 more
Caused by: java.lang.IllegalStateException: This store is read-only [1.4.191/2]
    at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773)
    at org.h2.mvstore.MVStore.commitAndSave(MVStore.java:1029)
    at org.h2.mvstore.MVStore.commit(MVStore.java:996)
    at org.h2.mvstore.db.TransactionStore.endTransaction(TransactionStore.java:456)
    at org.h2.mvstore.db.TransactionStore.commit(TransactionStore.java:364)
    at org.h2.mvstore.db.TransactionStore$Transaction.commit(TransactionStore.java:779)
    at org.modeshape.persistence.file.FileDb.txCommitted(FileDb.java:228)
    at org.modeshape.jcr.txn.Transactions$SimpleTransaction.commit(Transactions.java:501)
    at org.modeshape.jcr.txn.Transactions$TraceableSimpleTransaction.commit(Transactions.java:557)
    at org.modeshape.jcr.txn.Transactions$NestableThreadLocalTransaction.commit(Transactions.java:584)
    at org.modeshape.jcr.cache.document.WritableSessionCache.save(WritableSessionCache.java:568)
    at org.modeshape.jcr.cache.document.WritableSessionCache.save(WritableSessionCache.java:507)
    at org.modeshape.jcr.SystemContent.save(SystemContent.java:121)
    at org.modeshape.jcr.SystemNamespaceRegistry.register(SystemNamespaceRegistry.java:171)
    at org.modeshape.jcr.JcrRepository$RunningState.<init>(JcrRepository.java:1140)
    at org.modeshape.jcr.JcrRepository$RunningState.<init>(JcrRepository.java:936)
    at org.modeshape.jcr.JcrRepository.doStart(JcrRepository.java:372)
    at org.modeshape.jcr.JcrRepository.getStartupProblems(JcrRepository.java:286)
    at org.fcrepo.kernel.modeshape.spring.ModeShapeRepositoryFactoryBean.buildRepository(ModeShapeRepositoryFactoryBean.java:80)
    ... 35 more

07-Nov-2017 16:12:30.071 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
07-Nov-2017 16:12:30.739 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log ContextListener: contextInitialized()
07-Nov-2017 16:12:30.740 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log SessionListener: contextInitialized()

[Bethany Seeger]

Hi Devin, 

Yes – looks like the correct file.   From the looks of this line:  

07-Nov-2017 16:12:30.043 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.fcrepo.http.commons.FedoraContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'modeshapeRepofactory': Invocation of init method failed; nested exception is org.fcrepo.kernel.api.exception.RepositoryRuntimeException: java.lang.IllegalStateException: This store is read-only [1.4.191/2]

I have to wonder if your data location (‘/mnt/fedora-data’) has wrong permissions and tomcat can’t write there?   That directory should be owned and writable by tomcat. This is what my permissions look like for that directory: 

drwxr-xr-x   7 tomcat  tomcat   150 Aug 22 13:14 fcrepo4-data

-Bethany

From: <fedora-c...@googlegroups.com> on behalf of Devin Griffin <devin1...@gmail.com>
Reply-To: "fedora-c...@googlegroups.com" <fedora-c...@googlegroups.com>
Date: Tuesday, November 7, 2017 at 6:15 PM
To: Fedora Community <fedora-c...@googlegroups.com>
Subject: Re: [fedora-community] Could not resolve placeholder 'fcrepo.modeshape.configuration' Tomcat8 | CentOS

[Devin Griffin]

I just changed my permissions and it worked, thank you!