Issues with Tomcat8 unable to load OSCAR

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Issues with Tomcat8 unable to load OSCAR

Peter Hutten-Czapski-2
The following Catalina out shows that drugref loads but ocar doesn't
It seems to complain about version of slf4j but I have no idea if this is what it is and how to fix it.


[localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more
08-Jun-2017 13:31:37.337 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.common.web.OscarSpringContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more

2017-06-08 13:31:37,344 INFO  [ContextStartupListener:55] Server processes starting. context=/oscar
log4j:WARN No appenders could be found for logger (org.oscarehr.util.VmStat).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2017-06-08 13:31:37,364 ERROR [ContextStartupListener:89] Unexpected error.
java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.util.ContextStartupListener
 java.lang.RuntimeException: java.lang.NullPointerException
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:90)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    ... 13 more

08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
08-Jun-2017 13:31:37.394 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [/oscar] startup failed due to previous errors
2017-06-08 13:31:37,415 INFO  [ContextStartupListener:128] Server processes stopping. context=/oscar
[localhost-startStop-1] INFO org.quartz.simpl.SimpleThreadPool - Job execution threads will use class loader of thread: localhost-startStop-1
[localhost-startStop-1] INFO org.quartz.core.SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Quartz Scheduler v.1.8.5 created.
[localhost-startStop-1] INFO org.quartz.simpl.RAMJobStore - RAMJobStore initialized.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v1.8.5) 'DefaultQuartzScheduler' with instanceId 'NON_CLUSTERED'
  Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
  NOT STARTED.
  Currently in standby mode.
  Number of jobs executed: 0
  Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 2 threads.
  Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.

[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler 'DefaultQuartzScheduler' initialized from default resource file in Quartz package: 'quartz.properties'
[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler version: 1.8.5
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutting down.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED paused.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutdown complete.
08-Jun-2017 13:31:37.662 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
08-Jun-2017 13:31:37.686 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [org.oscarehr.util.VmStat] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.690 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [WaitListEmailThread Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.691 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [CaisiIntegratorUpdateTask Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.773 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/oscar.war has finished in 22,737 ms
08-Jun-2017 13:31:37.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/drugref.war
08-Jun-2017 13:31:37.818 WARNING [localhost-startStop-1] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property.
2017-06-08 13:31:39,122 INFO  [StartUp:55] contextInit called
2017-06-08 13:31:39,123 INFO  [StartUp:61] Looking for properties file at: /var/lib/tomcat8/drugref2.properties
2017-06-08 13:31:39,124 DEBUG [DrugrefProperties:54] DRUGREF PROPS CONSTRUCTOR
2017-06-08 13:31:39,126 DEBUG [DrugrefProperties:48] static initializer of drugrefproperties
2017-06-08 13:31:39,127 INFO  [StartUp:71] About to start Interactions checker with keynull
2017-06-08 13:31:40,246 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,260 DEBUG [Runtime:72] No cache marshaller found for id org.apache.openjpa.conf.MetaDataCacheMaintenance.
2017-06-08 13:31:40,421 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.BrokerFactory=jdbc, openjpa.BrokerImpl=non-finalizing, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,456 WARN  [Runtime:92] An error occurred while registering a ClassTransformer with PersistenceUnitInfo: name 'persistenceUnit', root URL [file:/var/lib/tomcat8/webapps/drugref/WEB-INF/classes]. The error is logged along with this warning. Load-time class transformation will not be available.
java.lang.IllegalStateException: Cannot apply class transformer without LoadTimeWeaver specified
    at org.springframework.orm.jpa.persistenceunit.SpringPersistenceUnitInfo.addTransformer(SpringPersistenceUnitInfo.java:109)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:126)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:53)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:290)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1571)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1509)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:296)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1117)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:922)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
    at org.drugref.util.SpringUtils.<clinit>(SpringUtils.java:43)
    at org.drugref.dinInteractionCheck.InteractionsChecker.<init>(InteractionsChecker.java:51)
    at org.drugref.dinInteractionCheck.InteractionsCheckerFactory.<clinit>(InteractionsCheckerFactory.java:45)
    at org.drugref.util.StartUp.contextInitialized(StartUp.java:72)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
2017-06-08 13:31:40,615 INFO  [StartUp:73] LAST LINE IN contextInitialized
08-Jun-2017 13:31:40.816 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/drugref.war has finished in 3,030 ms
08-Jun-2017 13:31:40.823 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /var/lib/tomcat8/webapps/ROOT
08-Jun-2017 13:31:41.366 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 543 ms
08-Jun-2017 13:31:41.372 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-openssl-nio-8443"]
08-Jun-2017 13:31:41.445 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 26649 ms


================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.

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Re: Issues with Tomcat8 unable to load OSCAR

Luiz Rufato

Ubuntu or Debian? What version?


Em 08-06-2017 14:34, Peter Hutten-Czapski escreveu:
The following Catalina out shows that drugref loads but ocar doesn't
It seems to complain about version of slf4j but I have no idea if this is what it is and how to fix it.


[localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more
08-Jun-2017 13:31:37.337 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.common.web.OscarSpringContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more

2017-06-08 13:31:37,344 INFO  [ContextStartupListener:55] Server processes starting. context=/oscar
log4j:WARN No appenders could be found for logger (org.oscarehr.util.VmStat).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2017-06-08 13:31:37,364 ERROR [ContextStartupListener:89] Unexpected error.
java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.util.ContextStartupListener
 java.lang.RuntimeException: java.lang.NullPointerException
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:90)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    ... 13 more

08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
08-Jun-2017 13:31:37.394 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [/oscar] startup failed due to previous errors
2017-06-08 13:31:37,415 INFO  [ContextStartupListener:128] Server processes stopping. context=/oscar
[localhost-startStop-1] INFO org.quartz.simpl.SimpleThreadPool - Job execution threads will use class loader of thread: localhost-startStop-1
[localhost-startStop-1] INFO org.quartz.core.SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Quartz Scheduler v.1.8.5 created.
[localhost-startStop-1] INFO org.quartz.simpl.RAMJobStore - RAMJobStore initialized.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v1.8.5) 'DefaultQuartzScheduler' with instanceId 'NON_CLUSTERED'
  Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
  NOT STARTED.
  Currently in standby mode.
  Number of jobs executed: 0
  Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 2 threads.
  Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.

[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler 'DefaultQuartzScheduler' initialized from default resource file in Quartz package: 'quartz.properties'
[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler version: 1.8.5
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutting down.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED paused.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutdown complete.
08-Jun-2017 13:31:37.662 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
08-Jun-2017 13:31:37.686 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [org.oscarehr.util.VmStat] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.690 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [WaitListEmailThread Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.691 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [CaisiIntegratorUpdateTask Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.773 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/oscar.war has finished in 22,737 ms
08-Jun-2017 13:31:37.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/drugref.war
08-Jun-2017 13:31:37.818 WARNING [localhost-startStop-1] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property.
2017-06-08 13:31:39,122 INFO  [StartUp:55] contextInit called
2017-06-08 13:31:39,123 INFO  [StartUp:61] Looking for properties file at: /var/lib/tomcat8/drugref2.properties
2017-06-08 13:31:39,124 DEBUG [DrugrefProperties:54] DRUGREF PROPS CONSTRUCTOR
2017-06-08 13:31:39,126 DEBUG [DrugrefProperties:48] static initializer of drugrefproperties
2017-06-08 13:31:39,127 INFO  [StartUp:71] About to start Interactions checker with keynull
2017-06-08 13:31:40,246 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,260 DEBUG [Runtime:72] No cache marshaller found for id org.apache.openjpa.conf.MetaDataCacheMaintenance.
2017-06-08 13:31:40,421 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.BrokerFactory=jdbc, openjpa.BrokerImpl=non-finalizing, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,456 WARN  [Runtime:92] An error occurred while registering a ClassTransformer with PersistenceUnitInfo: name 'persistenceUnit', root URL [file:/var/lib/tomcat8/webapps/drugref/WEB-INF/classes]. The error is logged along with this warning. Load-time class transformation will not be available.
java.lang.IllegalStateException: Cannot apply class transformer without LoadTimeWeaver specified
    at org.springframework.orm.jpa.persistenceunit.SpringPersistenceUnitInfo.addTransformer(SpringPersistenceUnitInfo.java:109)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:126)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:53)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:290)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1571)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1509)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:296)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1117)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:922)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
    at org.drugref.util.SpringUtils.<clinit>(SpringUtils.java:43)
    at org.drugref.dinInteractionCheck.InteractionsChecker.<init>(InteractionsChecker.java:51)
    at org.drugref.dinInteractionCheck.InteractionsCheckerFactory.<clinit>(InteractionsCheckerFactory.java:45)
    at org.drugref.util.StartUp.contextInitialized(StartUp.java:72)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
2017-06-08 13:31:40,615 INFO  [StartUp:73] LAST LINE IN contextInitialized
08-Jun-2017 13:31:40.816 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/drugref.war has finished in 3,030 ms
08-Jun-2017 13:31:40.823 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /var/lib/tomcat8/webapps/ROOT
08-Jun-2017 13:31:41.366 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 543 ms
08-Jun-2017 13:31:41.372 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-openssl-nio-8443"]
08-Jun-2017 13:31:41.445 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 26649 ms


================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.


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Re: Issues with Tomcat8 unable to load OSCAR

Peter Hutten-Czapski
Hi Luiz
I have installed Debian Stretch in virtualbox and am trying to make OSCAR 15 work with Tomcat 8.5

Configuration of VERSION=15-62~636
Server version: Apache Tomcat/8.5.14 (Debian)
Server built:   May 7 2017 22:17:52 UTC
Server number:  8.5.14.0
OS Name:        Linux
OS Version:     4.9.0-3-amd64
Architecture:   amd64
JVM Version:    1.8.0_131-8u131-b11-2-b11  (OpenJDK)
mysql  Ver 15.1 Distrib 10.1.23-MariaDB, for debian-linux-gnu (x86_64) using readline 5.2

drugref works fine now with my latest, but oscar, and its a lot more fancy coding, does not

================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.

On 8 June 2017 at 14:22, Luiz Rufato <[hidden email]> wrote:

Ubuntu or Debian? What version?


Em 08-06-2017 14:34, Peter Hutten-Czapski escreveu:
The following Catalina out shows that drugref loads but ocar doesn't
It seems to complain about version of slf4j but I have no idea if this is what it is and how to fix it.


[localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more
08-Jun-2017 13:31:37.337 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.common.web.OscarSpringContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more

2017-06-08 13:31:37,344 INFO  [ContextStartupListener:55] Server processes starting. context=/oscar
log4j:WARN No appenders could be found for logger (org.oscarehr.util.VmStat).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2017-06-08 13:31:37,364 ERROR [ContextStartupListener:89] Unexpected error.
java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.util.ContextStartupListener
 java.lang.RuntimeException: java.lang.NullPointerException
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:90)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    ... 13 more

08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
08-Jun-2017 13:31:37.394 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [/oscar] startup failed due to previous errors
2017-06-08 13:31:37,415 INFO  [ContextStartupListener:128] Server processes stopping. context=/oscar
[localhost-startStop-1] INFO org.quartz.simpl.SimpleThreadPool - Job execution threads will use class loader of thread: localhost-startStop-1
[localhost-startStop-1] INFO org.quartz.core.SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Quartz Scheduler v.1.8.5 created.
[localhost-startStop-1] INFO org.quartz.simpl.RAMJobStore - RAMJobStore initialized.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v1.8.5) 'DefaultQuartzScheduler' with instanceId 'NON_CLUSTERED'
  Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
  NOT STARTED.
  Currently in standby mode.
  Number of jobs executed: 0
  Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 2 threads.
  Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.

[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler 'DefaultQuartzScheduler' initialized from default resource file in Quartz package: 'quartz.properties'
[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler version: 1.8.5
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutting down.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED paused.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutdown complete.
08-Jun-2017 13:31:37.662 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
08-Jun-2017 13:31:37.686 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [org.oscarehr.util.VmStat] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.690 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [WaitListEmailThread Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.691 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [CaisiIntegratorUpdateTask Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.773 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/oscar.war has finished in 22,737 ms
08-Jun-2017 13:31:37.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/drugref.war
08-Jun-2017 13:31:37.818 WARNING [localhost-startStop-1] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property.
2017-06-08 13:31:39,122 INFO  [StartUp:55] contextInit called
2017-06-08 13:31:39,123 INFO  [StartUp:61] Looking for properties file at: /var/lib/tomcat8/drugref2.properties
2017-06-08 13:31:39,124 DEBUG [DrugrefProperties:54] DRUGREF PROPS CONSTRUCTOR
2017-06-08 13:31:39,126 DEBUG [DrugrefProperties:48] static initializer of drugrefproperties
2017-06-08 13:31:39,127 INFO  [StartUp:71] About to start Interactions checker with keynull
2017-06-08 13:31:40,246 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,260 DEBUG [Runtime:72] No cache marshaller found for id org.apache.openjpa.conf.MetaDataCacheMaintenance.
2017-06-08 13:31:40,421 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.BrokerFactory=jdbc, openjpa.BrokerImpl=non-finalizing, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,456 WARN  [Runtime:92] An error occurred while registering a ClassTransformer with PersistenceUnitInfo: name 'persistenceUnit', root URL [file:/var/lib/tomcat8/webapps/drugref/WEB-INF/classes]. The error is logged along with this warning. Load-time class transformation will not be available.
java.lang.IllegalStateException: Cannot apply class transformer without LoadTimeWeaver specified
    at org.springframework.orm.jpa.persistenceunit.SpringPersistenceUnitInfo.addTransformer(SpringPersistenceUnitInfo.java:109)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:126)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:53)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:290)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1571)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1509)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:296)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1117)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:922)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
    at org.drugref.util.SpringUtils.<clinit>(SpringUtils.java:43)
    at org.drugref.dinInteractionCheck.InteractionsChecker.<init>(InteractionsChecker.java:51)
    at org.drugref.dinInteractionCheck.InteractionsCheckerFactory.<clinit>(InteractionsCheckerFactory.java:45)
    at org.drugref.util.StartUp.contextInitialized(StartUp.java:72)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
2017-06-08 13:31:40,615 INFO  [StartUp:73] LAST LINE IN contextInitialized
08-Jun-2017 13:31:40.816 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/drugref.war has finished in 3,030 ms
08-Jun-2017 13:31:40.823 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /var/lib/tomcat8/webapps/ROOT
08-Jun-2017 13:31:41.366 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 543 ms
08-Jun-2017 13:31:41.372 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-openssl-nio-8443"]
08-Jun-2017 13:31:41.445 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 26649 ms


================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.


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Re: Issues with Tomcat8 unable to load OSCAR

Marc Dumontier
they must have some conflicting slf4j library which gets loaded first


Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)



On Thu, Jun 8, 2017 at 2:52 PM, Peter Hutten-Czapski <[hidden email]> wrote:
Hi Luiz
I have installed Debian Stretch in virtualbox and am trying to make OSCAR 15 work with Tomcat 8.5

Configuration of VERSION=15-62~636
Server version: Apache Tomcat/8.5.14 (Debian)
Server built:   May 7 2017 22:17:52 UTC
Server number:  8.5.14.0
OS Name:        Linux
OS Version:     4.9.0-3-amd64
Architecture:   amd64
JVM Version:    1.8.0_131-8u131-b11-2-b11  (OpenJDK)
mysql  Ver 15.1 Distrib 10.1.23-MariaDB, for debian-linux-gnu (x86_64) using readline 5.2

drugref works fine now with my latest, but oscar, and its a lot more fancy coding, does not

================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.

On 8 June 2017 at 14:22, Luiz Rufato <[hidden email]> wrote:

Ubuntu or Debian? What version?


Em 08-06-2017 14:34, Peter Hutten-Czapski escreveu:
The following Catalina out shows that drugref loads but ocar doesn't
It seems to complain about version of slf4j but I have no idea if this is what it is and how to fix it.


[localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more
08-Jun-2017 13:31:37.337 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.common.web.OscarSpringContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more

2017-06-08 13:31:37,344 INFO  [ContextStartupListener:55] Server processes starting. context=/oscar
log4j:WARN No appenders could be found for logger (org.oscarehr.util.VmStat).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2017-06-08 13:31:37,364 ERROR [ContextStartupListener:89] Unexpected error.
java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.util.ContextStartupListener
 java.lang.RuntimeException: java.lang.NullPointerException
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:90)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    ... 13 more

08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
08-Jun-2017 13:31:37.394 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [/oscar] startup failed due to previous errors
2017-06-08 13:31:37,415 INFO  [ContextStartupListener:128] Server processes stopping. context=/oscar
[localhost-startStop-1] INFO org.quartz.simpl.SimpleThreadPool - Job execution threads will use class loader of thread: localhost-startStop-1
[localhost-startStop-1] INFO org.quartz.core.SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Quartz Scheduler v.1.8.5 created.
[localhost-startStop-1] INFO org.quartz.simpl.RAMJobStore - RAMJobStore initialized.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v1.8.5) 'DefaultQuartzScheduler' with instanceId 'NON_CLUSTERED'
  Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
  NOT STARTED.
  Currently in standby mode.
  Number of jobs executed: 0
  Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 2 threads.
  Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.

[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler 'DefaultQuartzScheduler' initialized from default resource file in Quartz package: 'quartz.properties'
[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler version: 1.8.5
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutting down.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED paused.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutdown complete.
08-Jun-2017 13:31:37.662 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
08-Jun-2017 13:31:37.686 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [org.oscarehr.util.VmStat] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.690 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [WaitListEmailThread Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.691 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [CaisiIntegratorUpdateTask Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.773 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/oscar.war has finished in 22,737 ms
08-Jun-2017 13:31:37.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/drugref.war
08-Jun-2017 13:31:37.818 WARNING [localhost-startStop-1] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property.
2017-06-08 13:31:39,122 INFO  [StartUp:55] contextInit called
2017-06-08 13:31:39,123 INFO  [StartUp:61] Looking for properties file at: /var/lib/tomcat8/drugref2.properties
2017-06-08 13:31:39,124 DEBUG [DrugrefProperties:54] DRUGREF PROPS CONSTRUCTOR
2017-06-08 13:31:39,126 DEBUG [DrugrefProperties:48] static initializer of drugrefproperties
2017-06-08 13:31:39,127 INFO  [StartUp:71] About to start Interactions checker with keynull
2017-06-08 13:31:40,246 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,260 DEBUG [Runtime:72] No cache marshaller found for id org.apache.openjpa.conf.MetaDataCacheMaintenance.
2017-06-08 13:31:40,421 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.BrokerFactory=jdbc, openjpa.BrokerImpl=non-finalizing, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,456 WARN  [Runtime:92] An error occurred while registering a ClassTransformer with PersistenceUnitInfo: name 'persistenceUnit', root URL [file:/var/lib/tomcat8/webapps/drugref/WEB-INF/classes]. The error is logged along with this warning. Load-time class transformation will not be available.
java.lang.IllegalStateException: Cannot apply class transformer without LoadTimeWeaver specified
    at org.springframework.orm.jpa.persistenceunit.SpringPersistenceUnitInfo.addTransformer(SpringPersistenceUnitInfo.java:109)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:126)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:53)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:290)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1571)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1509)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:296)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1117)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:922)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
    at org.drugref.util.SpringUtils.<clinit>(SpringUtils.java:43)
    at org.drugref.dinInteractionCheck.InteractionsChecker.<init>(InteractionsChecker.java:51)
    at org.drugref.dinInteractionCheck.InteractionsCheckerFactory.<clinit>(InteractionsCheckerFactory.java:45)
    at org.drugref.util.StartUp.contextInitialized(StartUp.java:72)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
2017-06-08 13:31:40,615 INFO  [StartUp:73] LAST LINE IN contextInitialized
08-Jun-2017 13:31:40.816 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/drugref.war has finished in 3,030 ms
08-Jun-2017 13:31:40.823 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /var/lib/tomcat8/webapps/ROOT
08-Jun-2017 13:31:41.366 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 543 ms
08-Jun-2017 13:31:41.372 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-openssl-nio-8443"]
08-Jun-2017 13:31:41.445 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 26649 ms


================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.


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Re: Issues with Tomcat8 unable to load OSCAR

Marc Dumontier
We probably need to change pom.xml to make it 'provided'

not sure if it will have any ill effect on our side


On Thu, Jun 8, 2017 at 4:27 PM, Marc Dumontier <[hidden email]> wrote:
they must have some conflicting slf4j library which gets loaded first


Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)



On Thu, Jun 8, 2017 at 2:52 PM, Peter Hutten-Czapski <[hidden email]> wrote:
Hi Luiz
I have installed Debian Stretch in virtualbox and am trying to make OSCAR 15 work with Tomcat 8.5

Configuration of VERSION=15-62~636
Server version: Apache Tomcat/8.5.14 (Debian)
Server built:   May 7 2017 22:17:52 UTC
Server number:  8.5.14.0
OS Name:        Linux
OS Version:     4.9.0-3-amd64
Architecture:   amd64
JVM Version:    1.8.0_131-8u131-b11-2-b11  (OpenJDK)
mysql  Ver 15.1 Distrib 10.1.23-MariaDB, for debian-linux-gnu (x86_64) using readline 5.2

drugref works fine now with my latest, but oscar, and its a lot more fancy coding, does not

================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.

On 8 June 2017 at 14:22, Luiz Rufato <[hidden email]> wrote:

Ubuntu or Debian? What version?


Em 08-06-2017 14:34, Peter Hutten-Czapski escreveu:
The following Catalina out shows that drugref loads but ocar doesn't
It seems to complain about version of slf4j but I have no idea if this is what it is and how to fix it.


[localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more
08-Jun-2017 13:31:37.337 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.common.web.OscarSpringContextLoaderListener
 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring_jpa.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:567)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
    at org.oscarehr.common.web.OscarSpringContextLoader.createWebApplicationContext(OscarSpringContextLoader.java:101)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Lorg/slf4j/helpers/FormattingTuple;
    at org.slf4j.impl.SimpleLogger.formatAndLog(SimpleLogger.java:414)
    at org.slf4j.impl.SimpleLogger.info(SimpleLogger.java:546)
    at org.hibernate.cfg.annotations.Version.<clinit>(Version.java:15)
    at org.hibernate.cfg.AnnotationConfiguration.<clinit>(AnnotationConfiguration.java:78)
    at org.hibernate.ejb.Ejb3Configuration.<clinit>(Ejb3Configuration.java:107)
    at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:130)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
    ... 25 more

2017-06-08 13:31:37,344 INFO  [ContextStartupListener:55] Server processes starting. context=/oscar
log4j:WARN No appenders could be found for logger (org.oscarehr.util.VmStat).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2017-06-08 13:31:37,364 ERROR [ContextStartupListener:89] Unexpected error.
java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.oscarehr.util.ContextStartupListener
 java.lang.RuntimeException: java.lang.NullPointerException
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:90)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
    at org.oscarehr.util.SpringUtils.getBean(SpringUtils.java:66)
    at org.oscarehr.util.ContextStartupListener.createOscarProgramIfNecessary(ContextStartupListener.java:104)
    at org.oscarehr.util.ContextStartupListener.contextInitialized(ContextStartupListener.java:68)
    ... 13 more

08-Jun-2017 13:31:37.383 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
08-Jun-2017 13:31:37.394 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [/oscar] startup failed due to previous errors
2017-06-08 13:31:37,415 INFO  [ContextStartupListener:128] Server processes stopping. context=/oscar
[localhost-startStop-1] INFO org.quartz.simpl.SimpleThreadPool - Job execution threads will use class loader of thread: localhost-startStop-1
[localhost-startStop-1] INFO org.quartz.core.SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Quartz Scheduler v.1.8.5 created.
[localhost-startStop-1] INFO org.quartz.simpl.RAMJobStore - RAMJobStore initialized.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v1.8.5) 'DefaultQuartzScheduler' with instanceId 'NON_CLUSTERED'
  Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
  NOT STARTED.
  Currently in standby mode.
  Number of jobs executed: 0
  Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 2 threads.
  Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.

[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler 'DefaultQuartzScheduler' initialized from default resource file in Quartz package: 'quartz.properties'
[localhost-startStop-1] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler version: 1.8.5
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutting down.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED paused.
[localhost-startStop-1] INFO org.quartz.core.QuartzScheduler - Scheduler DefaultQuartzScheduler_$_NON_CLUSTERED shutdown complete.
08-Jun-2017 13:31:37.662 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
08-Jun-2017 13:31:37.686 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [org.oscarehr.util.VmStat] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.690 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [WaitListEmailThread Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.691 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [CaisiIntegratorUpdateTask Timer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)
 java.util.TimerThread.mainLoop(Timer.java:526)
 java.util.TimerThread.run(Timer.java:505)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.692 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [oscar] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:543)
08-Jun-2017 13:31:37.773 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/oscar.war has finished in 22,737 ms
08-Jun-2017 13:31:37.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/drugref.war
08-Jun-2017 13:31:37.818 WARNING [localhost-startStop-1] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property 'antiJARLocking' to 'true' did not find a matching property.
2017-06-08 13:31:39,122 INFO  [StartUp:55] contextInit called
2017-06-08 13:31:39,123 INFO  [StartUp:61] Looking for properties file at: /var/lib/tomcat8/drugref2.properties
2017-06-08 13:31:39,124 DEBUG [DrugrefProperties:54] DRUGREF PROPS CONSTRUCTOR
2017-06-08 13:31:39,126 DEBUG [DrugrefProperties:48] static initializer of drugrefproperties
2017-06-08 13:31:39,127 INFO  [StartUp:71] About to start Interactions checker with keynull
2017-06-08 13:31:40,246 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,260 DEBUG [Runtime:72] No cache marshaller found for id org.apache.openjpa.conf.MetaDataCacheMaintenance.
2017-06-08 13:31:40,421 DEBUG [Runtime:72] Setting the following properties from "?" into configuration: {openjpa.ConnectionFactory=org.apache.commons.dbcp.BasicDataSource@57740ad, openjpa.BrokerFactory=jdbc, openjpa.BrokerImpl=non-finalizing, openjpa.Compatibility=QuotedNumbersInQueries=true, openjpa.Log=log4j, openjpa.Id=persistenceUnit, openjpa.ClassResolver=org.apache.openjpa.persistence.PersistenceUnitInfoImpl$ClassResolverImpl@129690df, openjpa.MetaDataFactory=jpa(Files=/var/lib/tomcat8/webapps/drugref/WEB-INF/classes)}
2017-06-08 13:31:40,456 WARN  [Runtime:92] An error occurred while registering a ClassTransformer with PersistenceUnitInfo: name 'persistenceUnit', root URL [file:/var/lib/tomcat8/webapps/drugref/WEB-INF/classes]. The error is logged along with this warning. Load-time class transformation will not be available.
java.lang.IllegalStateException: Cannot apply class transformer without LoadTimeWeaver specified
    at org.springframework.orm.jpa.persistenceunit.SpringPersistenceUnitInfo.addTransformer(SpringPersistenceUnitInfo.java:109)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:126)
    at org.apache.openjpa.persistence.PersistenceProviderImpl.createContainerEntityManagerFactory(PersistenceProviderImpl.java:53)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:290)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1571)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1509)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:296)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1117)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:922)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
    at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
    at org.drugref.util.SpringUtils.<clinit>(SpringUtils.java:43)
    at org.drugref.dinInteractionCheck.InteractionsChecker.<init>(InteractionsChecker.java:51)
    at org.drugref.dinInteractionCheck.InteractionsCheckerFactory.<clinit>(InteractionsCheckerFactory.java:45)
    at org.drugref.util.StartUp.contextInitialized(StartUp.java:72)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
2017-06-08 13:31:40,615 INFO  [StartUp:73] LAST LINE IN contextInitialized
08-Jun-2017 13:31:40.816 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/drugref.war has finished in 3,030 ms
08-Jun-2017 13:31:40.823 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /var/lib/tomcat8/webapps/ROOT
08-Jun-2017 13:31:41.366 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 543 ms
08-Jun-2017 13:31:41.372 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-openssl-nio-8443"]
08-Jun-2017 13:31:41.445 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 26649 ms


================
Peter Hutten-Czapski
Haileybury Ontario

"The attitude that ‘if rural people want these services they’ll have to come to the city to get them’ is simply not acceptable…” (Newbery, 1999)

Before printing, think about the environment. Avant d' imprimer, pensez à l'environnement.


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--
Marc Dumontier
<a href="tel:(519)%20584-5601" value="+15195845601" target="_blank">519-584-5601
http://www.hxb.ca
http://www.oscarmcmaster.org




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