Coder Social home page Coder Social logo

jenspiegsa / openclinica Goto Github PK

View Code? Open in Web Editor NEW
8.0 4.0 6.0 57 KB

Dockerfile for OpenClinica.

Home Page: https://registry.hub.docker.com/u/piegsaj/openclinica/

License: GNU Affero General Public License v3.0

Shell 100.00%
docker dockerfile openclinica

openclinica's Introduction

OpenClinica 3.13 via Docker

The OpenClinica Community edition is free and open source and is distributed under the GNU LGPL license.

This repository contains the Dockerfile, a startup script and the following instructions for running a Docker container which you can use to give OpenClinica a try. An image built with this Dockerfile is available on Docker Hub.

IMPORTANT: This image is meant for trying out OpenClinica and not meant for running a production server or for storing important study data.

Setup

0. Install Docker

  • Follow the installation instructions for your host system
  • If you are running Docker on VirtualBox: the maximum RAM size can be adjusted through the user interface of VirtualBox (run it from the start menu, stop the virtual machine, change the configuration to e.g. 4096MB, close it and start the virtual machine using docker-machine)

1. Create a database init script

  • Create a file init-db.sh that adds a user and a database for OpenClinica to PostgreSQL:
#!/bin/bash
set -e

psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" <<-EOSQL
    CREATE ROLE clinica LOGIN ENCRYPTED PASSWORD 'clinica' SUPERUSER NOINHERIT NOCREATEDB NOCREATEROLE;
    CREATE DATABASE openclinica WITH ENCODING='UTF8' OWNER=clinica;
EOSQL
  • Please adjust the database password

2. Start a PostgreSQL database server

  • This expects the init-db.sh script residing in the current directory
docker container run --name ocdb -d -v ocdb-data:/var/lib/postgresql/data \
 -v $PWD/init-db.sh:/docker-entrypoint-initdb.d/init-db.sh \
 -p 5432:5432 \
 -e POSTGRES_INITDB_ARGS="-E 'UTF-8' --locale=POSIX" \
 -e POSTGRES_PASSWORD=postgres123 \
 postgres:9.5
  • Please change the root database password

3. Start Tomcat serving OpenClinica and OpenClinica-ws

docker container run --name oc -h oc -d -v oc-data:/usr/local/tomcat/openclinica.data \
 -p 80:8080 \
 -e LOG_LEVEL=INFO \
 -e TZ=UTC-1 \
 -e DB_TYPE=postgres \
 -e DB_HOST=192.168.99.100 \
 -e DB_NAME=openclinica \
 -e DB_USER=clinica \
 -e DB_PASS=clinica \
 -e DB_PORT=5432 \
 -e SUPPORT_URL="https://www.openclinica.com/community-edition-open-source-edc/" \
 piegsaj/openclinica:oc-3.13
  • Adjust DB_HOST and passwords accordingly
  • The environment variables for log level and timezone are optional here.

4. Run OpenClinica

Operation

To show the OpenClinica logs:

docker container logs -f oc

To backup a database dump to the current directory on the host:

echo "postgres123" | docker container run -i --rm \
 --link ocdb:ocdb \
 -v $PWD:/tmp \
 postgres:9.5 sh -c '\
 pg_dump -h ocdb -p $OCDB_PORT_5432_TCP_PORT -U postgres -F tar -v openclinica \
 > /tmp/ocdb_pg_dump_$(date +%Y-%m-%d_%H-%M-%S).tar'

To backup the OpenClinica data folder to the current directory on the host:

docker container run --rm \
 -v oc-data:/tomcat/openclinica.data \
 -v $PWD:/tmp \
 piegsaj/openclinica:oc-3.13 \
 tar cvf /tmp/oc_data_backup_$(date +%Y-%m-%d_%H-%M-%S).tar /tomcat/openclinica.data

Contribute

Feedback is welcome. The source is available on Github. Please report any issues.

openclinica's People

Contributors

jenspiegsa avatar

Stargazers

avatar avatar avatar avatar avatar avatar avatar avatar

Watchers

avatar avatar avatar avatar

Forkers

apsl patrick-werner dahoba testnobody abelzhu tianzilei

openclinica's Issues

Error from the oc container log

Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version: Apache Tomcat/7.0.77
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built: Mar 28 2017 16:01:48 UTC
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number: 7.0.77.0
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name: Linux
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version: 3.10.0-514.2.2.el7.x86_64
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture: amd64
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version: 1.8.0_121-8u121-b13-1~bpo8+1-b13
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor: Oracle Corporation
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE: /usr/local/tomcat
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME: /usr/local/tomcat
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1280m
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseParallelGC
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/local/tomcat/endorsed
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/local/tomcat
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/local/tomcat
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
Jun 10, 2017 9:21:11 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: Loaded APR based Apache Tomcat Native library 1.2.12 using APR version 1.5.1.
Jun 10, 2017 9:21:11 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
Jun 10, 2017 9:21:11 PM org.apache.catalina.core.AprLifecycleListener initializeSSL
INFO: OpenSSL successfully initialized (OpenSSL 1.1.0e 16 Feb 2017)
Jun 10, 2017 9:21:11 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-apr-8080"]
Jun 10, 2017 9:21:11 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-apr-8009"]
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 426 ms
Jun 10, 2017 9:21:11 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Jun 10, 2017 9:21:11 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.77
Jun 10, 2017 9:21:11 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat/webapps/OpenClinica
Jun 10, 2017 9:21:15 PM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
Jun 10, 2017 9:21:16 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jun 10, 2017 9:21:33 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.akaza.openclinica.dao.core.OCContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesService' defined in class path resource [org/akaza/openclinica/applicationContext-core-service.xml]: Cannot resolve reference to bean 'viewNotesDao' while setting bean property 'viewNotesDao'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesDao' defined in class path resource [org/akaza/openclinica/applicationContext-core-hibernate.xml]: Cannot resolve reference to bean 'queryStore' while setting bean property 'queryStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1325)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1086)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:580)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
at org.akaza.openclinica.dao.core.OCContextLoaderListener.contextInitialized(OCContextLoaderListener.java:38)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5118)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1260)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:2002)
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:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesDao' defined in class path resource [org/akaza/openclinica/applicationContext-core-hibernate.xml]: Cannot resolve reference to bean 'queryStore' while setting bean property 'queryStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1325)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1086)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 29 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
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:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 39 more
Caused by: org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.akaza.openclinica.dao.QueryStore.resolveDbFolder(QueryStore.java:89)
at org.akaza.openclinica.dao.QueryStore.init(QueryStore.java:41)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1544)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1485)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
... 46 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.akaza.openclinica.dao.QueryStore.resolveDbFolder(QueryStore.java:80)
... 54 more
Caused by: org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:152)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:125)
at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3g.AbstractJdbc3gConnection.(AbstractJdbc3gConnection.java:22)
at org.postgresql.jdbc4.AbstractJdbc4Connection.(AbstractJdbc4Connection.java:32)
at org.postgresql.jdbc4.Jdbc4Connection.(Jdbc4Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:393)
at org.postgresql.Driver.connect(Driver.java:267)
at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
... 57 more
Caused by: java.net.NoRouteToHostException: No route to host (Host unreachable)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.(Socket.java:434)
at java.net.Socket.(Socket.java:211)
at org.postgresql.core.PGStream.(PGStream.java:62)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:76)
... 69 more

Jun 10, 2017 9:21:33 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.akaza.openclinica.control.OCServletContextListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesService' defined in class path resource [org/akaza/openclinica/applicationContext-core-service.xml]: Cannot resolve reference to bean 'viewNotesDao' while setting bean property 'viewNotesDao'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesDao' defined in class path resource [org/akaza/openclinica/applicationContext-core-hibernate.xml]: Cannot resolve reference to bean 'queryStore' while setting bean property 'queryStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1325)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1086)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:580)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
at org.akaza.openclinica.dao.core.OCContextLoaderListener.contextInitialized(OCContextLoaderListener.java:38)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5118)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1260)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:2002)
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:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesDao' defined in class path resource [org/akaza/openclinica/applicationContext-core-hibernate.xml]: Cannot resolve reference to bean 'queryStore' while setting bean property 'queryStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1325)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1086)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 29 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
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:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 39 more
Caused by: org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.akaza.openclinica.dao.QueryStore.resolveDbFolder(QueryStore.java:89)
at org.akaza.openclinica.dao.QueryStore.init(QueryStore.java:41)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1544)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1485)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
... 46 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.akaza.openclinica.dao.QueryStore.resolveDbFolder(QueryStore.java:80)
... 54 more
Caused by: org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:152)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:125)
at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3g.AbstractJdbc3gConnection.(AbstractJdbc3gConnection.java:22)
at org.postgresql.jdbc4.AbstractJdbc4Connection.(AbstractJdbc4Connection.java:32)
at org.postgresql.jdbc4.Jdbc4Connection.(Jdbc4Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:393)
at org.postgresql.Driver.connect(Driver.java:267)
at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
... 57 more
Caused by: java.net.NoRouteToHostException: No route to host (Host unreachable)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.(Socket.java:434)
at java.net.Socket.(Socket.java:211)
at org.postgresql.core.PGStream.(PGStream.java:62)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:76)
... 69 more

Jun 10, 2017 9:21:33 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Jun 10, 2017 9:21:33 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/OpenClinica] startup failed due to previous errors
Jun 10, 2017 9:21:33 PM org.apache.catalina.core.StandardContext listenerStop
SEVERE: Exception sending context destroyed event to listener instance of class org.akaza.openclinica.control.OCServletContextListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesService' defined in class path resource [org/akaza/openclinica/applicationContext-core-service.xml]: Cannot resolve reference to bean 'viewNotesDao' while setting bean property 'viewNotesDao'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesDao' defined in class path resource [org/akaza/openclinica/applicationContext-core-hibernate.xml]: Cannot resolve reference to bean 'queryStore' while setting bean property 'queryStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1325)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1086)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:580)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
at org.akaza.openclinica.dao.core.OCContextLoaderListener.contextInitialized(OCContextLoaderListener.java:38)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5118)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1260)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:2002)
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:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewNotesDao' defined in class path resource [org/akaza/openclinica/applicationContext-core-hibernate.xml]: Cannot resolve reference to bean 'queryStore' while setting bean property 'queryStore'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1325)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1086)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 29 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'queryStore' defined in class path resource [org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
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:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 39 more
Caused by: org.springframework.beans.factory.BeanInitializationException: Unable to read datasource information; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.akaza.openclinica.dao.QueryStore.resolveDbFolder(QueryStore.java:89)
at org.akaza.openclinica.dao.QueryStore.init(QueryStore.java:41)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1544)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1485)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
... 46 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.akaza.openclinica.dao.QueryStore.resolveDbFolder(QueryStore.java:80)
... 54 more
Caused by: org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:152)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:125)
at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3g.AbstractJdbc3gConnection.(AbstractJdbc3gConnection.java:22)
at org.postgresql.jdbc4.AbstractJdbc4Connection.(AbstractJdbc4Connection.java:32)
at org.postgresql.jdbc4.Jdbc4Connection.(Jdbc4Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:393)
at org.postgresql.Driver.connect(Driver.java:267)
at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
... 57 more
Caused by: java.net.NoRouteToHostException: No route to host (Host unreachable)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.(Socket.java:434)
at java.net.Socket.(Socket.java:211)
at org.postgresql.core.PGStream.(PGStream.java:62)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:76)
... 69 more

Jun 10, 2017 9:21:33 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Jun 10, 2017 9:21:33 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
SEVERE: The web application [/OpenClinica] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Jun 10, 2017 9:21:33 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [net.sf.ehcache.CacheManager@6ace6461] but has failed to stop it. This is very likely to create a memory leak.
Jun 10, 2017 9:21:33 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Jun 10, 2017 9:21:33 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat/webapps/OpenClinica has finished in 21,305 ms
Jun 10, 2017 9:21:33 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat/webapps/OpenClinica-ws
Jun 10, 2017 9:21:35 PM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
Jun 10, 2017 9:21:36 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jun 10, 2017 9:21:41 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'liquibase' defined in URL [jar:file:/usr/local/tomcat/webapps/OpenClinica-ws/WEB-INF/lib/OpenClinica-core-3.13.jar!/org/akaza/openclinica/applicationContext-core-db.xml]: Invocation of init method failed; nested exception is liquibase.exception.JDBCException: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
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$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:281)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:563)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5118)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1260)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:2002)
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:745)
Caused by: liquibase.exception.JDBCException: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at liquibase.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:216)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1477)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
... 27 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (The connection attempt failed.)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at liquibase.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:211)
... 29 more
Caused by: org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:152)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:125)
at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3g.AbstractJdbc3gConnection.(AbstractJdbc3gConnection.java:22)
at org.postgresql.jdbc4.AbstractJdbc4Connection.(AbstractJdbc4Connection.java:32)
at org.postgresql.jdbc4.Jdbc4Connection.(Jdbc4Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:393)
at org.postgresql.Driver.connect(Driver.java:267)
at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
... 32 more
Caused by: java.net.NoRouteToHostException: No route to host (Host unreachable)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.(Socket.java:434)
at java.net.Socket.(Socket.java:211)
at org.postgresql.core.PGStream.(PGStream.java:62)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:76)
... 44 more

Jun 10, 2017 9:21:41 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Jun 10, 2017 9:21:41 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/OpenClinica-ws] startup failed due to previous errors
Jun 10, 2017 9:21:41 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Jun 10, 2017 9:21:41 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
SEVERE: The web application [/OpenClinica-ws] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Jun 10, 2017 9:21:41 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/OpenClinica-ws] appears to have started a thread named [net.sf.ehcache.CacheManager@99a08b2] but has failed to stop it. This is very likely to create a memory leak.
Jun 10, 2017 9:21:41 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [/OpenClinica-ws] appears to have started a thread named [Timer-1] but has failed to stop it. This is very likely to create a memory leak.
Jun 10, 2017 9:21:41 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat/webapps/OpenClinica-ws has finished in 7,809 ms
Jun 10, 2017 9:21:41 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-apr-8080"]
Jun 10, 2017 9:21:41 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-apr-8009"]
Jun 10, 2017 9:21:41 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 29161 ms

Can not connect to server

@JensPiegsa Thanks for providing this Docker image.

I've followed your procedures in your README and have successfully launched the OC server under docker. However, I have not been successful in connecting to the 127.0.0.1:8080/OpenClinica service page. The DB_HOST for Postgres was changed to 127.0.0.1 and port mapping to 8080:8080.

I've tried both connecting to my local machine's ip: 192.168.2.2 as well as 127.0.0.1 but all were refused to connection.

Any suggestions on how to further proceed? Thank you for your time!

Sean

Docker script used

sudo docker container run --name oc -h oc -d -v oc-data:/usr/local/tomcat/openclinica.data \
 -p 8080:8080 \
 -e LOG_LEVEL=INFO \
 -e TZ=UTC-1 \
 -e DB_TYPE=postgres \
 -e DB_HOST=127.0.0.1 \
 -e DB_NAME=openclinica \
 -e DB_USER=clinica \
 -e DB_PASS=password \
 -e DB_PORT=5432 \
 -e SUPPORT_URL="https://www.openclinica.com/community-edition-open-source-edc/" \
 piegsaj/openclinica:oc-3.13

Docker listing

-> % sudo docker container ls                                                                    
CONTAINER ID        IMAGE                         COMMAND                  CREATED             STATUS              PORTS                    NAMES
25b8e74e43ba        piegsaj/openclinica:oc-3.13   "/run.sh"                4 minutes ago       Up 4 minutes        0.0.0.0:8080->8080/tcp   oc
4a46778d76ad        postgres:9.5                  "docker-entrypoint..."   About an hour ago   Up About an hour    0.0.0.0:5432->5432/tcp   ocdb

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.