Open Specimen Upgrade to v3.4.1

Shanthan · April 24, 2017, 5:18pm

Hi

I have build and deployed the OpenSpecimen version 3.4.1 from source according to the instructions on https://openspecimen.atlassian.net/wiki/pages/viewpage.action?pageId=1115955

Following error found in the Tomcat log:

OpenSpecimen, a Krishagni Product
Build Version :
Build Date : Mon Apr 17 14:39:47 CDT 2017
Commit :
Present Time : Mon Apr 24 11:52:30 CDT 2017

log4j:ERROR Could not read configuration file from URL [file:/D:/OS_V2.5/tomcat-
as/bin/OS_V2.5os-plugins].
java.io.FileNotFoundException: D:\OS_V2.5\tomcat-as\bin\OS_V2.5os-plugins (The s
ystem cannot find the file specified)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(Unknown Source)
at java.io.FileInputStream.(Unknown Source)
at java.io.FileInputStream.(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown So
urce)
at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurato
r.java:524)
at org.apache.log4j.PropertyConfigurator.configure(PropertyConfigurator.
java:415)
at com.krishagni.catissueplus.core.init.AppServletContextListener.initLo
gging(AppServletContextListener.java:104)
at com.krishagni.catissueplus.core.init.AppServletContextListener.contex
tInitialized(AppServletContextListener.java:62)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContex
t.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContex
t.java:5528)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase
.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:87
7)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)

    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090

)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:
1900)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
log4j:ERROR Ignoring configuration file [file:/D:/OS_V2.5/tomcat-as/bin/OS_V2.5o
s-plugins].
log4j:WARN No appenders could be found for logger (com.krishagni.catissueplus.co
re.init.AppServletContextListener).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more in
fo.
Apr 24, 2017 11:52:32 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Apr 24, 2017 11:52:32 AM org.apache.catalina.util.SessionIdGeneratorBase createS
ecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRN
G] took [149] milliseconds.
Apr 24, 2017 11:52:32 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/openspecimen] startup failed due to previous errors
Apr 24, 2017 11:52:32 AM org.apache.catalina.loader.WebappClassLoader clearRefer
encesThreads
SEVERE: The web application [/openspecimen] appears to have started a thread nam
ed [FileWatchdog] but has failed to stop it. This is very likely to create a mem
ory leak.
Apr 24, 2017 11:52:32 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive D:\OS_V2.5\tomcat-as\webapps\openspe
cimen.war has finished in 7,124 ms
Apr 24, 2017 11:52:32 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\backup
Apr 24, 2017 11:52:32 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\backu
p has finished in 245 ms
Apr 24, 2017 11:52:32 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\docs
Apr 24, 2017 11:52:33 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\docs
has finished in 231 ms
Apr 24, 2017 11:52:33 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\examples
Apr 24, 2017 11:52:33 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\examp
les has finished in 438 ms
Apr 24, 2017 11:52:33 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\host-mana
ger
Apr 24, 2017 11:52:33 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\host-
manager has finished in 236 ms
Apr 24, 2017 11:52:33 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\manager
Apr 24, 2017 11:52:34 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\manag
er has finished in 242 ms
Apr 24, 2017 11:52:34 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\ROOT
Apr 24, 2017 11:52:34 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\ROOT
has finished in 224 ms
Apr 24, 2017 11:52:34 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler [“http-bio-8080”]
Apr 24, 2017 11:52:34 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler [“ajp-bio-8009”]
Apr 24, 2017 11:52:34 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 8900 ms

Chetan_Khilosiya · April 25, 2017, 10:57am

Hi @Shanthan,
According to error log, if your plugin folder name is os-plugins then the ‘/’ is missing in path given which should be
D:/OS_V2.5/tomcat-as/bin/OS_V2.5/os-plugins

Shanthan · April 27, 2017, 2:44pm

Hi @Chetan_Khilosiya

Thanks for your reply, I struggle now with this error:

OpenSpecimen, a Krishagni Product
Build Version :
Build Date : Mon Apr 17 14:39:47 CDT 2017
Commit :
Present Time : Thu Apr 27 09:31:13 CDT 2017

log4j:WARN No appenders could be found for logger (com.krishagni.catissueplus.co
re.init.AppServletContextListener).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more in
fo.
log4j:ERROR Could not read configuration file [/D:/OS_V2.5/os-plugins/].
java.io.FileNotFoundException: D:\OS_V2.5\os-plugins (Access is denied)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(Unknown Source)
at java.io.FileInputStream.(Unknown Source)
at java.io.FileInputStream.(Unknown Source)
at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurato
r.java:372)
at org.apache.log4j.PropertyWatchdog.doOnChange(PropertyConfigurator.jav
a:922)
at org.apache.log4j.helpers.FileWatchdog.checkAndConfigure(FileWatchdog.
java:89)
at org.apache.log4j.helpers.FileWatchdog.(FileWatchdog.java:58)
at org.apache.log4j.PropertyWatchdog.(PropertyConfigurator.java:91
4)
at org.apache.log4j.PropertyConfigurator.configureAndWatch(PropertyConfi
gurator.java:461)
at org.apache.log4j.PropertyConfigurator.configureAndWatch(PropertyConfi
gurator.java:443)
at com.krishagni.catissueplus.core.init.AppServletContextListener.initLo
gging(AppServletContextListener.java:107)
at com.krishagni.catissueplus.core.init.AppServletContextListener.contex
tInitialized(AppServletContextListener.java:62)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContex
t.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContex
t.java:5528)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase
.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:87
7)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)

    at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.jav

a:1258)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig
.java:1918)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
log4j:ERROR Ignoring configuration file [/D:/OS_V2.5/os-plugins/].
Apr 27, 2017 9:31:16 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Apr 27, 2017 9:31:16 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/openspecimen] startup failed due to previous errors
Apr 27, 2017 9:31:16 AM org.apache.catalina.loader.WebappClassLoader clearRefere
ncesThreads
SEVERE: The web application [/openspecimen] appears to have started a thread nam
ed [FileWatchdog] but has failed to stop it. This is very likely to create a mem
ory leak.
Apr 27, 2017 9:31:16 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\opens
pecimen has finished in 6,547 ms
Apr 27, 2017 9:31:16 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory D:\OS_V2.5\tomcat-as\webapps\ROOT
Apr 27, 2017 9:31:16 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory D:\OS_V2.5\tomcat-as\webapps\ROOT
has finished in 297 ms
Apr 27, 2017 9:31:16 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler [“http-bio-8080”]
Apr 27, 2017 9:31:16 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler [“ajp-bio-8009”]
Apr 27, 2017 9:31:16 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 9203 ms

Chetan_Khilosiya · May 1, 2017, 11:27am

Hi @Shanthan,

According to log, it seems you are specifying path of os-plugins directory as
value of app_log_conf property. Property app_log_conf is used to
specify custom logging configuration. Leave this property value empty.
Please provide os-plugins directory path as value of plugin_dir
property.

Shanthan · May 2, 2017, 8:12pm

Thanks @Chetan_Khilosiya, we were able to resolve the issue but we have another issue.

May 02, 2017 2:43:14 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
May 02, 2017 2:43:15 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
May 02, 2017 2:43:15 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
May 02, 2017 2:43:15 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: attributeAdded(‘org.apache.jasper.compiler.TldLocationsCache’, ‘org.apache.jasper.compiler.TldLocationsCache@34ce2640’)
May 02, 2017 2:44:19 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
May 02, 2017 2:44:19 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
May 02, 2017 2:44:25 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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.ChangeLogParseException: Error Reading Migration File: class path resource [db/db-os-changelog-master-Upgrade.xml] cannot be resolved to URL because it does not exist
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1514)
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$1.getObject(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: liquibase.exception.ChangeLogParseException: Error Reading Migration File: class path resource [db/db-os-changelog-master-Upgrade.xml] cannot be resolved to URL because it does not exist
at liquibase.parser.core.xml.XMLChangeLogSAXParser.parseToNode(XMLChangeLogSAXParser.java:112)
at liquibase.parser.core.xml.AbstractChangeLogParser.parse(AbstractChangeLogParser.java:17)
at liquibase.Liquibase.getDatabaseChangeLog(Liquibase.java:215)
at liquibase.Liquibase.update(Liquibase.java:192)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
… 25 more
Caused by: java.io.FileNotFoundException: class path resource [db/db-os-changelog-master-Upgrade.xml] cannot be resolved to URL because it does not exist
at org.springframework.core.io.ClassPathResource.getURL(ClassPathResource.java:186)
at liquibase.integration.spring.SpringLiquibase$SpringResourceOpener.getResourcesAsStream(SpringLiquibase.java:156)
at liquibase.util.StreamUtil.singleInputStream(StreamUtil.java:181)
at liquibase.parser.core.xml.XMLChangeLogSAXParser.parseToNode(XMLChangeLogSAXParser.java:93)
… 32 more

vpawar · May 4, 2017, 9:43am

Hi @Shanthan

It seems you’ve built OpenSpecimen using deployment_type=Upgrade. Please note “upgrade” (all lower case) should be used only if your DB instance was first created using NCI caTissue. If your database was created from scratch by OpenSpecimen then you need to set deployment_type=fresh (all lower case). Please choose an appropriate value for the deployment_type property, rebuild, deploy and start OpenSpecimen.

Thanks

Shanthan · May 4, 2017, 8:44pm

Thanks for the response @vpawar, we have a another issue. can you please take a look.

May 04, 2017 12:14:35 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
May 04, 2017 12:14:35 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
May 04, 2017 12:14:42 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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/db-os-changelog-pre-2.0-oracle.xml::1427201434763-2::OpenSpecimen:
Reason: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1514)
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$1.getObject(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

Caused by: liquibase.exception.MigrationFailedException: Migration failed for change set db/db-os-changelog-pre-2.0-oracle.xml::1427201434763-2::OpenSpecimen:
Reason: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at liquibase.changelog.ChangeSet.execute(ChangeSet.java:586)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
at liquibase.Liquibase.update(Liquibase.java:200)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
... 25 more

Caused by: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:316)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:122)
at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1227)
at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1210)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:550)
... 32 more

Caused by: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at oracle.jdbc.driver.SQLStateMapping.newSQLException(SQLStateMapping.java:91)
at oracle.jdbc.driver.DatabaseError.newSQLException(DatabaseError.java:133)
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:206)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:455)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:413)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:1034)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:183)
at oracle.jdbc.driver.T4CStatement.executeForRows(T4CStatement.java:942)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1222)
at oracle.jdbc.driver.OracleStatement.executeInternal(OracleStatement.java:1770)
at oracle.jdbc.driver.OracleStatement.execute(OracleStatement.java:1739)
at oracle.jdbc.driver.OracleStatementWrapper.execute(OracleStatementWrapper.java:299)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:314)
... 37 more

May 04, 2017 12:14:42 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
May 04, 2017 12:14:43 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
May 04, 2017 12:14:43 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
May 04, 2017 12:14:43 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: attributeAdded(‘org.apache.jasper.compiler.TldLocationsCache’, ‘org.apache.jasper.compiler.TldLocationsCache@6615a7a9’)
May 04, 2017 2:13:14 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
May 04, 2017 2:13:21 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
May 04, 2017 2:14:13 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
May 04, 2017 2:14:14 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
May 04, 2017 2:14:20 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 ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/db-os-changelog-pre-2.0-oracle.xml::1427201434763-2::OpenSpecimen:
Reason: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1514)
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$1.getObject(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5528)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1090)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1900)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

Caused by: liquibase.exception.MigrationFailedException: Migration failed for change set db/db-os-changelog-pre-2.0-oracle.xml::1427201434763-2::OpenSpecimen:
Reason: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at liquibase.changelog.ChangeSet.execute(ChangeSet.java:586)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:43)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:73)
at liquibase.Liquibase.update(Liquibase.java:200)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:402)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:366)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
... 25 more

Caused by: liquibase.exception.DatabaseException: java.sql.SQLSyntaxErrorException: ORA-00955: name is already used by an existing object

at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:316)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:122)
at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1227)
at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1210)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:550)
... 32 more