Unable to setup icescrum on ubuntu

[nag.abhishek]

Hi,

I am unable to setup icescrum on ubuntu server.

Following are the details:

Ubuntu server : Ubuntu 13.04
Java version “1.7.0_80”
Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
Tomcat Apache : Apache Tomcat/7.0.35

Logs:

catalina.out :

INFO: Deploying web application archive /var/lib/tomcat7/webapps/icescrum.war
Aug 05, 2015 10:32:42 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/var/lib/tomcat7/webapps/icescrum/WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar) – jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Server Timezone : Asia/Kolkata
log dir : logs
——————————————————–
*** No external configuration file defined (icescrum_config_location). ***
(*) grails.config.locations = []
——————————————————–

Configuring iceScrum plugin Embedded …
… finished configuring iceScrum plugin Embedded

Configuring iceScrum plugin Cloud storage …
… finished configuring iceScrum plugin Cloud storage

Configuring Spring Security Core …
… finished configuring Spring Security Core

Configuring Spring Security ACL …
… finished configuring Spring Security ACL

Configuring iceScrum plugin management …
… finished configuring iceScrum plugin management

Configuring iceScrum plugin chat …
… finished configuring iceScrum plugin chat
Aug 05, 2015 10:33:09 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Aug 05, 2015 10:33:09 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/icescrum] startup failed due to previous errors

Thanks

[Vincent Barrier]

Hello,

Could you provide stacktrace.log and catalina.out?

Regards;

[nag.abhishek]

Hi,

Below are the log generate

catalina.out :

INFO: Deploying web application archive /var/lib/tomcat7/webapps/icescrum.war
Aug 05, 2015 11:55:47 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/var/lib/tomcat7/webapps/icescrum/WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Server Timezone : Asia/Kolkata
log dir : logs
--------------------------------------------------------
*** No external configuration file defined (icescrum_config_location). ***
(*) grails.config.locations = []
--------------------------------------------------------

Configuring iceScrum plugin Cloud storage ...
... finished configuring iceScrum plugin Cloud storage

Configuring iceScrum plugin Embedded ...
... finished configuring iceScrum plugin Embedded

Configuring Spring Security Core ...
... finished configuring Spring Security Core

Configuring Spring Security ACL ...
... finished configuring Spring Security ACL

Configuring iceScrum plugin management ...
... finished configuring iceScrum plugin management

Configuring iceScrum plugin chat ...
... finished configuring iceScrum plugin chat
Aug 05, 2015 11:56:14 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Aug 05, 2015 11:56:14 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/icescrum] startup failed due to previous errors

stacktrace.log :

2015-08-05 11:56:14,142 [localhost-startStop-1] ERROR StackTrace  - Sanitizing stacktrace:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'messageSource': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: org.hsqldb.jdbcDriver
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
	at org.codehaus.groovy.grails.commons.spring.ReloadAwareAutowireCapableBeanFactory.doCreateBean(ReloadAwareAutowireCapableBeanFactory.java:135)
	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:194)
	at org.springframework.context.support.AbstractApplicationContext.initMessageSource(AbstractApplicationContext.java:755)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:413)
	at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:154)
	at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:164)
	at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:124)
	at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:120)
	at org.codehaus.groovy.grails.web.context.GrailsContextLoader.createWebApplicationContext(GrailsContextLoader.java:73)
	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:4797)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5291)
	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:633)
	at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:977)
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1655)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: org.hsqldb.jdbcDriver
	... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: org.hsqldb.jdbcDriver
	... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: org.hsqldb.jdbcDriver
	... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: org.hsqldb.jdbcDriver
	... 5 more
Caused by: org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: org.hsqldb.jdbcDriver
	... 5 more
Caused by: java.sql.SQLException: org.hsqldb.jdbcDriver
	at com.sun.proxy.$Proxy58.getMetaData(Unknown Source)
	... 5 more
Caused by: java.lang.ClassNotFoundException: org.hsqldb.jdbcDriver
	at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:270)
	... 6 more

Thanks

[Nicolas Noullet]

Hi,

As indicated in the documentation:
Tomcat 7 (7.0.23 or greater), recommended: you need to remove the tomcatDir/lib/tomcat-jdbc.jar library.

Did you remove the tomcat-jdbc jar?

[nag.abhishek]

Hi,

When I removed the tomcat-jdbc jar, following logs were generated.

catalina.out

INFO: Deploying web application archive /var/lib/tomcat7/webapps/icescrum.war
Aug 05, 2015 1:17:59 PM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/var/lib/tomcat7/webapps/icescrum/WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Server Timezone : Asia/Kolkata
log dir : logs
--------------------------------------------------------
*** No external configuration file defined (icescrum_config_location). ***
(*) grails.config.locations = []
--------------------------------------------------------

Configuring iceScrum plugin Cloud storage ...
... finished configuring iceScrum plugin Cloud storage

Configuring iceScrum plugin Embedded ...
... finished configuring iceScrum plugin Embedded

Configuring Spring Security Core ...
... finished configuring Spring Security Core

Configuring Spring Security ACL ...
... finished configuring Spring Security ACL

Configuring iceScrum plugin management ...
... finished configuring iceScrum plugin management

Configuring iceScrum plugin chat ...
... finished configuring iceScrum plugin chat
Aug 05, 2015 1:18:25 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Aug 05, 2015 1:18:25 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/icescrum] startup failed due to previous errors
Aug 05, 2015 1:18:25 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/icescrum] registered the JDBC driver [org.hsqldb.jdbcDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

stacktrace.log

2015-08-05 13:18:25,860 [localhost-startStop-1] ERROR StackTrace  - Sanitizing stacktrace:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'messageSource': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
	at org.codehaus.groovy.grails.commons.spring.ReloadAwareAutowireCapableBeanFactory.doCreateBean(ReloadAwareAutowireCapableBeanFactory.java:135)
	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:194)
	at org.springframework.context.support.AbstractApplicationContext.initMessageSource(AbstractApplicationContext.java:755)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:413)
	at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:154)
	at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:164)
	at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:124)
	at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:120)
	at org.codehaus.groovy.grails.web.context.GrailsContextLoader.createWebApplicationContext(GrailsContextLoader.java:73)
	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:4797)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5291)
	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:633)
	at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:977)
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1655)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Cannot resolve reference to bean 'hibernateProperties' while setting bean property 'hibernateProperties'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateProperties': Cannot resolve reference to bean 'dialectDetector' while setting bean property 'properties' with key [hibernate.dialect]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dialectDetector': Invocation of init method failed; nested exception is org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	... 5 more
Caused by: org.springframework.jdbc.support.MetaDataAccessException: Error while extracting DatabaseMetaData; nested exception is java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	... 5 more
Caused by: java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)
	at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
	at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
	at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
	at org.hsqldb.jdbcDriver.connect(Unknown Source)
	at com.sun.proxy.$Proxy58.getMetaData(Unknown Source)
	... 5 more

[Nicolas Noullet]

Thanks for your answer, removing the tomcat-jdbc jar was the right thing to do.

This new error indicates that the default database files cannot be created because the user who starts Tomcat lacks write permissions in the directory where iceScrum attempts to create them.

These files are created by default in the startup path (the directory from where you start Tomcat). Can you try adding the appropriate permissions?

[nag.abhishek]

Hi,

I checked it has appropriate permissions also I am starting tomcat as root user.

[Nicolas Noullet]

Well, that’s unexpected… The error message clearly states that it is a permission issue:
java.sql.SQLException: File input/output error prodDba.properties java.io.FileNotFoundException: prodDba.properties.new (Permission denied)

Another approach to solving your problem would consist in defining the connection to another DBMS, e.g. MySQL, if available. This solution provides the benefit that it will ensure that you use a safe DBMS (the default one, HSQLDB, is not reliable and should not be used for production).

If you really want to stay with HSQLDB and if additional checks on permissions give no solution then I can provide a way to manually set where iceScrum will create the HSQLDB file.

[nag.abhishek]

Hi,

I want to stay with HSQLDB, can you provide me the way to configure manually.

Thanks

[Nicolas Noullet]

Hi,

To do so, you will have to change the database connection URL by updating / adding a specific setting in the config.groovy file: dataSource.url

Here is its default value:
dataSource.url = "jdbc:hsqldb:file:prodDba;shutdown=true"

Here prodDba is the name of the DB and the name of the files which will be created. You can update the path like so to create them in the user home:
dataSource.url = "jdbc:hsqldb:file:~/prodDba;shutdown=true"

You can choose whatever path you want, however, I can’t guarantee that such change will fix your issue.

[Author]

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