[apollo] Can't deploy webapp

[matthew couchman (JIC)]

Hi,

I'm getting an error which I can't make sense of when I try and deploy the .war file generated by .apollo deploy. Tomcat's localhost.yyyy-mm-dd.log says:

Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more

Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: attributeAdded('org.apache.jasper.compiler.TldLocationsCache', '***@6465b52e')

The Tomcat examples seem to work OK on my local server. Any help much appreciated.

Thanks,

Matt.

[Nathan Dunn]

Usually we get this if the database isn’t started or can’t be connected to. If you are using PostgreSQL, there are some trouble-shooting tips here:

http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html <http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html>

Nathan

Post by matthew couchman (JIC)
Hi,
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
The Tomcat examples seem to work OK on my local server. Any help much appreciated.
Thanks,
Matt.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

[matthew couchman (JIC)]

Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?

Many thanks,

Matt.


From: apollo-***@lists.lbl.gov [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 11 April 2016 17:39
To: ***@lists.lbl.gov
Subject: Re: [apollo] Can't deploy webapp


Usually we get this if the database isn’t started or can’t be connected to. If you are using PostgreSQL, there are some trouble-shooting tips here:

http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html

Nathan

On Apr 11, 2016, at 9:34 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> wrote:

Hi,

I’m getting an error which I can’t make sense of when I try and deploy the .war file generated by .apollo deploy. Tomcat’s localhost.yyyy-mm-dd.log says:

Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more

Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: attributeAdded('org.apache.jasper.compiler.TldLocationsCache', '***@6465b52e')

The Tomcat examples seem to work OK on my local server. Any help much appreciated.

Thanks,

Matt.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to ***@lists.lbl.gov<mailto:***@lists.lbl.gov> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

[Nathan Dunn]

MySQL is perfectly good. We test that database as well. That error is indicative of a database connection failure. So a few thoughts:

0 - compare your apollo-config.groovy to sample-mysql-apollo-config.groovy and see if you notice anything important
1 - make sure that you have the database created. Apollo will create the schema, but it needs a blank database.
2 - try using “./apollo run-local” with your specified apollo-config.groovy. If that doesn’t work, try without the apollo-config.groovy in place (do an ./apollo clean first though) (it will use H2). This will use a “local” tomcat.
3 - post your config file (without passwords) and we can take a look. If you know the version of mysql that might help as well (in case we have the wrong jdbc connector).
4 - ps -ef | grep java . . . just double-check that you are not running two servers

Hope this helps,

Nathan

Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html <http://webapollo.readthedocs.org/en/latest/ExampleBuild.html> but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?
Many thanks,
Matt.
Sent: 11 April 2016 17:39
Subject: Re: [apollo] Can't deploy webapp
http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html <http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html>
Nathan
Hi,
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
The Tomcat examples seem to work OK on my local server. Any help much appreciated.
Thanks,
Matt.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

[matthew couchman (JIC)]

Hi Nathan,

Thanks for your help again. Looking in the logs it seems that Apollo is connecting OK to apollo-production but that it then attempts to connect to apollo-production-chado which doesn’t exist yet. Should the install process build apollo-production-chado? Would it work if I commented the chado section out of apollo-config.groovy? Is there a mysql dump of the chado schema available to download?

Many thanks,

Matt.


From: apollo-***@lists.lbl.gov [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 13 April 2016 16:50
To: ***@lists.lbl.gov
Subject: Re: [apollo] Can't deploy webapp


MySQL is perfectly good. We test that database as well. That error is indicative of a database connection failure. So a few thoughts:

0 - compare your apollo-config.groovy to sample-mysql-apollo-config.groovy and see if you notice anything important
1 - make sure that you have the database created. Apollo will create the schema, but it needs a blank database.
2 - try using “./apollo run-local” with your specified apollo-config.groovy. If that doesn’t work, try without the apollo-config.groovy in place (do an ./apollo clean first though) (it will use H2). This will use a “local” tomcat.
3 - post your config file (without passwords) and we can take a look. If you know the version of mysql that might help as well (in case we have the wrong jdbc connector).
4 - ps -ef | grep java . . . just double-check that you are not running two servers

Hope this helps,

Nathan

On Apr 13, 2016, at 4:59 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> wrote:

Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?

Many thanks,

Matt.


From: apollo-***@lists.lbl.gov<mailto:apollo-***@lists.lbl.gov> [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 11 April 2016 17:39
To: ***@lists.lbl.gov<mailto:***@lists.lbl.gov>
Subject: Re: [apollo] Can't deploy webapp


Usually we get this if the database isn’t started or can’t be connected to. If you are using PostgreSQL, there are some trouble-shooting tips here:

http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html

Nathan

On Apr 11, 2016, at 9:34 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> wrote:

Hi,

I’m getting an error which I can’t make sense of when I try and deploy the .war file generated by .apollo deploy. Tomcat’s localhost.yyyy-mm-dd.log says:

Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more

Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: attributeAdded('org.apache.jasper.compiler.TldLocationsCache', '***@6465b52e')

The Tomcat examples seem to work OK on my local server. Any help much appreciated.

Thanks,

Matt.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to ***@lists.lbl.gov<mailto:***@lists.lbl.gov> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to ***@lists.lbl.gov<mailto:***@lists.lbl.gov> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

[Lbl]

If you are using MySQL I would comment out the chado section. Chado is optimized to work with PostgreSQL afaik though I'm certain you could get it working on MySQL. You could point the Apollo side to a MySQL instance and the chado one to a PostgreSQL instance. Furthermore you can set it up without chado now but add it later.

Nathan

Post by matthew couchman (JIC)
Hi Nathan,
Thanks for your help again. Looking in the logs it seems that Apollo is connecting OK to apollo-production but that it then attempts to connect to apollo-production-chado which doesn’t exist yet. Should the install process build apollo-production-chado? Would it work if I commented the chado section out of apollo-config.groovy? Is there a mysql dump of the chado schema available to download?
Many thanks,
Matt.
Sent: 13 April 2016 16:50
Subject: Re: [apollo] Can't deploy webapp
0 - compare your apollo-config.groovy to sample-mysql-apollo-config.groovy and see if you notice anything important
1 - make sure that you have the database created. Apollo will create the schema, but it needs a blank database.
2 - try using “./apollo run-local” with your specified apollo-config.groovy. If that doesn’t work, try without the apollo-config.groovy in place (do an ./apollo clean first though) (it will use H2). This will use a “local” tomcat.
3 - post your config file (without passwords) and we can take a look. If you know the version of mysql that might help as well (in case we have the wrong jdbc connector).
4 - ps -ef | grep java . . . just double-check that you are not running two servers
Hope this helps,
Nathan
Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?
Many thanks,
Matt.
Sent: 11 April 2016 17:39
Subject: Re: [apollo] Can't deploy webapp
http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html
Nathan
Hi,
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
The Tomcat examples seem to work OK on my local server. Any help much appreciated.
Thanks,
Matt.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Nathan Dunn]

The chado configuration in the mysql (and h2) sample configuration was there in error in the master and has been removed.

If you are looking for an immediate production release, you might want to use our latest 2.0.2 release: https://github.com/GMOD/Apollo/releases/tag/2.0.2 <https://github.com/GMOD/Apollo/releases/tag/2.0.2>.

If you need / want Chado integration we will be releasing 2.0.3 based off of master, so please continue to give us feedback on that.

Nathan

Post by matthew couchman (JIC)
Hi Nathan,
Thanks for your help again. Looking in the logs it seems that Apollo is connecting OK to apollo-production but that it then attempts to connect to apollo-production-chado which doesn’t exist yet. Should the install process build apollo-production-chado? Would it work if I commented the chado section out of apollo-config.groovy? Is there a mysql dump of the chado schema available to download?
Many thanks,
Matt.
Sent: 13 April 2016 16:50
Subject: Re: [apollo] Can't deploy webapp
0 - compare your apollo-config.groovy to sample-mysql-apollo-config.groovy and see if you notice anything important
1 - make sure that you have the database created. Apollo will create the schema, but it needs a blank database.
2 - try using “./apollo run-local” with your specified apollo-config.groovy. If that doesn’t work, try without the apollo-config.groovy in place (do an ./apollo clean first though) (it will use H2). This will use a “local” tomcat.
3 - post your config file (without passwords) and we can take a look. If you know the version of mysql that might help as well (in case we have the wrong jdbc connector).
4 - ps -ef | grep java . . . just double-check that you are not running two servers
Hope this helps,
Nathan
Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html <http://webapollo.readthedocs.org/en/latest/ExampleBuild.html> but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?
Many thanks,
Matt.
Sent: 11 April 2016 17:39
Subject: Re: [apollo] Can't deploy webapp
http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html <http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html>
Nathan
Hi,
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
The Tomcat examples seem to work OK on my local server. Any help much appreciated.
Thanks,
Matt.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

[matthew couchman (JIC)]

Commenting out the chado stuff has fixed it. Many thanks for your help and patience.

From: apollo-***@lists.lbl.gov [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 15 April 2016 15:55
To: ***@lists.lbl.gov
Subject: Re: [apollo] Can't deploy webapp


The chado configuration in the mysql (and h2) sample configuration was there in error in the master and has been removed.

If you are looking for an immediate production release, you might want to use our latest 2.0.2 release: https://github.com/GMOD/Apollo/releases/tag/2.0.2.

If you need / want Chado integration we will be releasing 2.0.3 based off of master, so please continue to give us feedback on that.

Nathan

On Apr 15, 2016, at 7:23 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> wrote:

Hi Nathan,

Thanks for your help again. Looking in the logs it seems that Apollo is connecting OK to apollo-production but that it then attempts to connect to apollo-production-chado which doesn’t exist yet. Should the install process build apollo-production-chado? Would it work if I commented the chado section out of apollo-config.groovy? Is there a mysql dump of the chado schema available to download?

Many thanks,

Matt.


From: apollo-***@lists.lbl.gov<mailto:apollo-***@lists.lbl.gov> [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 13 April 2016 16:50
To: ***@lists.lbl.gov<mailto:***@lists.lbl.gov>
Subject: Re: [apollo] Can't deploy webapp


MySQL is perfectly good. We test that database as well. That error is indicative of a database connection failure. So a few thoughts:

0 - compare your apollo-config.groovy to sample-mysql-apollo-config.groovy and see if you notice anything important
1 - make sure that you have the database created. Apollo will create the schema, but it needs a blank database.
2 - try using “./apollo run-local” with your specified apollo-config.groovy. If that doesn’t work, try without the apollo-config.groovy in place (do an ./apollo clean first though) (it will use H2). This will use a “local” tomcat.
3 - post your config file (without passwords) and we can take a look. If you know the version of mysql that might help as well (in case we have the wrong jdbc connector).
4 - ps -ef | grep java . . . just double-check that you are not running two servers

Hope this helps,

Nathan

On Apr 13, 2016, at 4:59 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> wrote:

Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?

Many thanks,

Matt.


From: apollo-***@lists.lbl.gov<mailto:apollo-***@lists.lbl.gov> [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 11 April 2016 17:39
To: ***@lists.lbl.gov<mailto:***@lists.lbl.gov>
Subject: Re: [apollo] Can't deploy webapp


Usually we get this if the database isn’t started or can’t be connected to. If you are using PostgreSQL, there are some trouble-shooting tips here:

http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html

Nathan

On Apr 11, 2016, at 9:34 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> wrote:

Hi,

I’m getting an error which I can’t make sense of when I try and deploy the .war file generated by .apollo deploy. Tomcat’s localhost.yyyy-mm-dd.log says:

Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more

Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: attributeAdded('org.apache.jasper.compiler.TldLocationsCache', '***@6465b52e')

The Tomcat examples seem to work OK on my local server. Any help much appreciated.

Thanks,

Matt.



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[Nathan Dunn]

No problem. Our doc was wrong so thanks for finding that.

Nathan

Post by matthew couchman (JIC)
Commenting out the chado stuff has fixed it. Many thanks for your help and patience.
Sent: 15 April 2016 15:55
Subject: Re: [apollo] Can't deploy webapp
The chado configuration in the mysql (and h2) sample configuration was there in error in the master and has been removed.
If you are looking for an immediate production release, you might want to use our latest 2.0.2 release: https://github.com/GMOD/Apollo/releases/tag/2.0.2 <https://github.com/GMOD/Apollo/releases/tag/2.0.2>.
If you need / want Chado integration we will be releasing 2.0.3 based off of master, so please continue to give us feedback on that.
Nathan
Hi Nathan,
Thanks for your help again. Looking in the logs it seems that Apollo is connecting OK to apollo-production but that it then attempts to connect to apollo-production-chado which doesn’t exist yet. Should the install process build apollo-production-chado? Would it work if I commented the chado section out of apollo-config.groovy? Is there a mysql dump of the chado schema available to download?
Many thanks,
Matt.
Sent: 13 April 2016 16:50
Subject: Re: [apollo] Can't deploy webapp
0 - compare your apollo-config.groovy to sample-mysql-apollo-config.groovy and see if you notice anything important
1 - make sure that you have the database created. Apollo will create the schema, but it needs a blank database.
2 - try using “./apollo run-local” with your specified apollo-config.groovy. If that doesn’t work, try without the apollo-config.groovy in place (do an ./apollo clean first though) (it will use H2). This will use a “local” tomcat.
3 - post your config file (without passwords) and we can take a look. If you know the version of mysql that might help as well (in case we have the wrong jdbc connector).
4 - ps -ef | grep java . . . just double-check that you are not running two servers
Hope this helps,
Nathan
Thanks for your help again Nathan. I’m more familiar with MySQL so I tried following the example at http://webapollo.readthedocs.org/en/latest/ExampleBuild.html <http://webapollo.readthedocs.org/en/latest/ExampleBuild.html> but i’m seeing the same error. I think some of the problem is my inexperience with Tomcat. Does Tomcat capture any details of the specific problem with the connection?
Many thanks,
Matt.
Sent: 11 April 2016 17:39
Subject: Re: [apollo] Can't deploy webapp
http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html <http://webapollo.readthedocs.org/en/latest/PostgreSQLSetup.html>
Nathan
Hi,
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Apr 11, 2016 5:24:53 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': 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': Invocation of init method failed; nested exception is java.lang.NullPointerException
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 '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': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
Apr 11, 2016 5:25:00 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Apr 11, 2016 5:25:01 PM org.apache.catalina.core.ApplicationContext log
The Tomcat examples seem to work OK on my local server. Any help much appreciated.
Thanks,
Matt.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>