Problem deploying webapollo while upgrading

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Problem deploying webapollo while upgrading

carlos vargas
Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 




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Re: Problem deploying webapollo while upgrading

nathandunn

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



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 [hidden email] | 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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Problem deploying webapollo while upgrading

carlos vargas
Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



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 [hidden email] | 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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Problem deploying webapollo while upgrading

nathandunn

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Problem deploying webapollo while upgrading

carlos vargas
Dear Nathan,

I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:


NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more

Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15218 ms

Thank you!
Carlos


On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Problem deploying webapollo while upgrading

nathandunn

Carlos,

Unsupported major.minor version 52.0

This typically means that the tomcat version you are runnings is probably running Java 7, but we have forced you to install Java / JDK 8 to compile and run. 

A couple things you can do:

- remove java 7 (unless you need it)
- in your environment set     JAVA_HOME to the Java 8 JDK (not the JRE) e.g., on Ubuntu . .    JAVA_HOME/usr/lib/jvm/java-8-openjdk-amd64 

That should do the trick (knock on wood).  

Either way, I’ll update the docs to clarify both of these as both of these issues have come up before. 

Thanks,

Nathan

On Feb 9, 2017, at 4:34 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:


NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more

Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15218 ms

Thank you!
Carlos


On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Problem deploying webapollo while upgrading

carlos vargas
Dear Nathan,

Completely removing all other java versions indeed worked, thanks a lot! However, I am having the same issue I was having with 2.0.2, I am still unable to display the reference sequence (genome and aminoacids on six frames). On switching to a new region they appear as a flash but then they just appear as a "loading" message. I think this is totally unrelated, want me to start a new message thread?

Thanks a lot!
Carlos 

On Fri, Feb 10, 2017 at 2:34 AM, Nathan Dunn <[hidden email]> wrote:

Carlos,

Unsupported major.minor version 52.0

This typically means that the tomcat version you are runnings is probably running Java 7, but we have forced you to install Java / JDK 8 to compile and run. 

A couple things you can do:

- remove java 7 (unless you need it)
- in your environment set     JAVA_HOME to the Java 8 JDK (not the JRE) e.g., on Ubuntu . .    JAVA_HOME/usr/lib/jvm/java-8-openjdk-amd64 

That should do the trick (knock on wood).  

Either way, I’ll update the docs to clarify both of these as both of these issues have come up before. 

Thanks,

Nathan

On Feb 9, 2017, at 4:34 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:


NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more

Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15218 ms

Thank you!
Carlos


On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



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Re: Problem deploying webapollo while upgrading

carlos vargas
Dear Nathan,

I thought this issue could be memory related, but it seems it has to do with the configuration in the trackList.json file. Upon loading webapollo I am still unable to see the reference track, but if I change the configuration (using the edit track configuration option) I am able to see it along with the six frames, however it is only a temporary  solution, for each time I change the page I am using I lose the configuration.
I have tried editing the information regarding the Reference sequence track in the trackList.json file, however, when I reload apollo (restarting tomcat) the track configuration is the same as before. Is there a trick to modify the Reference sequence track permenently in the trackList.json file?

Thanks for your time,
Carlos 

On Fri, Feb 10, 2017 at 12:03 PM, carlos vargas <[hidden email]> wrote:
Dear Nathan,

Completely removing all other java versions indeed worked, thanks a lot! However, I am having the same issue I was having with 2.0.2, I am still unable to display the reference sequence (genome and aminoacids on six frames). On switching to a new region they appear as a flash but then they just appear as a "loading" message. I think this is totally unrelated, want me to start a new message thread?

Thanks a lot!
Carlos 

On Fri, Feb 10, 2017 at 2:34 AM, Nathan Dunn <[hidden email]> wrote:

Carlos,

Unsupported major.minor version 52.0

This typically means that the tomcat version you are runnings is probably running Java 7, but we have forced you to install Java / JDK 8 to compile and run. 

A couple things you can do:

- remove java 7 (unless you need it)
- in your environment set     JAVA_HOME to the Java 8 JDK (not the JRE) e.g., on Ubuntu . .    JAVA_HOME/usr/lib/jvm/java-8-openjdk-amd64 

That should do the trick (knock on wood).  

Either way, I’ll update the docs to clarify both of these as both of these issues have come up before. 

Thanks,

Nathan

On Feb 9, 2017, at 4:34 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:


NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more

Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15218 ms

Thank you!
Carlos


On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Problem deploying webapollo while upgrading

nathandunn

Carlos,

If you update the trackList.json file, those changes should be “permanent”, with the exception that the first time you create an organism it loads all of the sequences into the database for that organism / genome.  

If the changes are significant, for example you changed the genome or sequence names, you’ll likely have to import it as another organism so that it is in-sync. 

BTW, what were you changing in the configuration to get it to work? 

Nathan

On Feb 10, 2017, at 8:07 AM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I thought this issue could be memory related, but it seems it has to do with the configuration in the trackList.json file. Upon loading webapollo I am still unable to see the reference track, but if I change the configuration (using the edit track configuration option) I am able to see it along with the six frames, however it is only a temporary  solution, for each time I change the page I am using I lose the configuration.
I have tried editing the information regarding the Reference sequence track in the trackList.json file, however, when I reload apollo (restarting tomcat) the track configuration is the same as before. Is there a trick to modify the Reference sequence track permenently in the trackList.json file?

Thanks for your time,
Carlos 

On Fri, Feb 10, 2017 at 12:03 PM, carlos vargas <[hidden email]> wrote:
Dear Nathan,

Completely removing all other java versions indeed worked, thanks a lot! However, I am having the same issue I was having with 2.0.2, I am still unable to display the reference sequence (genome and aminoacids on six frames). On switching to a new region they appear as a flash but then they just appear as a "loading" message. I think this is totally unrelated, want me to start a new message thread?

Thanks a lot!
Carlos 

On Fri, Feb 10, 2017 at 2:34 AM, Nathan Dunn <[hidden email]> wrote:

Carlos,

Unsupported major.minor version 52.0

This typically means that the tomcat version you are runnings is probably running Java 7, but we have forced you to install Java / JDK 8 to compile and run. 

A couple things you can do:

- remove java 7 (unless you need it)
- in your environment set     JAVA_HOME to the Java 8 JDK (not the JRE) e.g., on Ubuntu . .    JAVA_HOME/usr/lib/jvm/java-8-openjdk-amd64 

That should do the trick (knock on wood).  

Either way, I’ll update the docs to clarify both of these as both of these issues have come up before. 

Thanks,

Nathan

On Feb 9, 2017, at 4:34 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:


NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more

Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15218 ms

Thank you!
Carlos


On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



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Re: Problem deploying webapollo while upgrading

carlos vargas
Dear Nathan,

I tried replacing entirely the Reference sequence block. On my trackList.json file it is set as:

      {
         "seqType" : "dna",
         "key" : "Reference sequence",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "chunkSize" : 20000,
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "type" : "SequenceTrack",
         "category" : "Reference sequence"
      }

and if I try to edit the config from the browser I see the following:

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "maxFeatureScreenDensity": 100000,
  "maxHeight": 1000,
  "style": {
    "arrowheadClass": null,
    "className": "{type}",
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "minSubfeatureWidth": 1,
    "maxDescriptionLength": 70,
    "showLabels": false,
    "label": "name,id",
    "description": "note, description",
    "centerChildrenVertically": false,
    "renderClassName": null,
    "subfeatureClasses": {
      "UTR": "webapollo-UTR",
      "CDS": "webapollo-CDS",
      "exon": "container-100pct",
      "intron": null,
      "wholeCDS": null,
      "start_codon": null,
      "stop_codon": null,
      "match_part": "darkblue-80pct"
    },
    "uniqueIdField": "id"
  },
  "hooks": {},
  "events": {},
  "menuTemplate": null,
  "ignoreFeatureFilter": true,
  "pinned": true,
  "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
  "chunkSize": 20000,
  "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
  "label": "DNA",
  "type": "WebApollo/View/Track/AnnotSequenceTrack",
  "category": "Reference sequence",
  "key": "Reference sequence",
  "seqType": "dna",
  "index": 1,
  "compress": 0,
  "subfeatures": 1,
  "metadata": {}
}

On http://www.yeastgenome.org I saw a different configuration that was displaying both the genome and the six frames which is the following:

{
  "maxExportSpan": 500000,
  "showForwardStrand": true,
  "showReverseStrand": true,
  "showTranslation": true,
  "category": "Reference sequence",
  "type": "JBrowse/View/Track/Sequence",
  "key": "Reference sequence",
  "storeClass": "JBrowse/Store/Sequence/StaticChunked",
  "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
  "label": "DNA",
  "chunkSize": 20000,
  "style": {},
  "metadata": {}
}

If I try replacing the configuration on the browser, using the configuration from the yeast and only changing the baseUrl, I do get what I want, but it is not permanent. Therefore I tried replacing the block in the trackList.json file but it seems to override the changes and keeps the same configuration. However, it does seem to be using the trackList.json file because removing a bracket (or breaking the format in any other way) causes the browser to display an error message.

Thank you for your time!
Carlos

On Fri, Feb 10, 2017 at 6:24 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If you update the trackList.json file, those changes should be “permanent”, with the exception that the first time you create an organism it loads all of the sequences into the database for that organism / genome.  

If the changes are significant, for example you changed the genome or sequence names, you’ll likely have to import it as another organism so that it is in-sync. 

BTW, what were you changing in the configuration to get it to work? 

Nathan

On Feb 10, 2017, at 8:07 AM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I thought this issue could be memory related, but it seems it has to do with the configuration in the trackList.json file. Upon loading webapollo I am still unable to see the reference track, but if I change the configuration (using the edit track configuration option) I am able to see it along with the six frames, however it is only a temporary  solution, for each time I change the page I am using I lose the configuration.
I have tried editing the information regarding the Reference sequence track in the trackList.json file, however, when I reload apollo (restarting tomcat) the track configuration is the same as before. Is there a trick to modify the Reference sequence track permenently in the trackList.json file?

Thanks for your time,
Carlos 

On Fri, Feb 10, 2017 at 12:03 PM, carlos vargas <[hidden email]> wrote:
Dear Nathan,

Completely removing all other java versions indeed worked, thanks a lot! However, I am having the same issue I was having with 2.0.2, I am still unable to display the reference sequence (genome and aminoacids on six frames). On switching to a new region they appear as a flash but then they just appear as a "loading" message. I think this is totally unrelated, want me to start a new message thread?

Thanks a lot!
Carlos 

On Fri, Feb 10, 2017 at 2:34 AM, Nathan Dunn <[hidden email]> wrote:

Carlos,

Unsupported major.minor version 52.0

This typically means that the tomcat version you are runnings is probably running Java 7, but we have forced you to install Java / JDK 8 to compile and run. 

A couple things you can do:

- remove java 7 (unless you need it)
- in your environment set     JAVA_HOME to the Java 8 JDK (not the JRE) e.g., on Ubuntu . .    JAVA_HOME/usr/lib/jvm/java-8-openjdk-amd64 

That should do the trick (knock on wood).  

Either way, I’ll update the docs to clarify both of these as both of these issues have come up before. 

Thanks,

Nathan

On Feb 9, 2017, at 4:34 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:


NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more
Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
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:745)
Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
at java.lang.Class.getDeclaredFields(Class.java:1819)
... 5 more

Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15218 ms

Thank you!
Carlos


On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances. 

However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.   

If neither version is working then I would:

- recreate your old database from the backup you made (hopefully)
- load ONLY the newly built tomcat as a war file

The new code will attempt to update the server. 

If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:


log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
    debug ‘grails.app’
}
and redump the catalina.out

Nathan

On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:

Dear Nathan,

Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).

INFO: Starting service Catalina
Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 14376 ms
Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks a lot!
Carlos

On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:

Carlos,

To clarify a few things:

1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ? 

2 - You built test.war with the same apollo-config.groovy file you used for your older installation?

3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.

4 - What do your tomcat logs look like (often in a file called catalina.out)?

Thanks,

Nathan

On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:

Hello everyone,

I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!

Best,
Carlos 



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Re: Problem deploying webapollo while upgrading

nathandunn

Carlos,

I don’t know if I’m following correctly or not.  

I guess I have a few thoughts:

0 - Just to double-check, you should ONLY see the reference track when you are zoomed in nearly all of the way in Apollo (to see sequences).  Conversely, in JBrowse it is always on.  Both by design.

1 - You shouldn’t have to mess with the baseUrl.  Typically, if its local to my instance, I just configure it locally.  e.g., (where your trackList.json is) /opt/apollo/yeast/   On the organism tab for that organism, the directory should be the same.  

2 - if its remote, that is fine.  Its possible that you are getting CORS issues.  If you look at your javascript or network console, you’ll see an error mentioning that.  You would have to lookup how to fix that on your server if need be. Maybe there is another error on the console?

3 - Its possible you generated the data incorrectly?   If you load the same data via JBrowse does it work?   If you don’t want to have Apache configured, you can use SimpleHttpServer within the “yeast” JSON directory:

python -m SimpleHTTPServer 8000

http://localhost/

and confirm that you see the yeast data.  

If you point Apollo to that same directory it should work.  

If it works in JBrowse, but not apollo, then you might try creating a new Organism (named something else) that points to the exact same directory and see if it doesn’t work.  


Nathan

> On Feb 10, 2017, at 9:34 AM, carlos vargas <[hidden email]> wrote:
>
> Dear Nathan,
>
> I tried replacing entirely the Reference sequence block. On my trackList.json file it is set as:
>
>       {
>          "seqType" : "dna",
>          "key" : "Reference sequence",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "chunkSize" : 20000,
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
>          "label" : "DNA",
>          "type" : "SequenceTrack",
>          "category" : "Reference sequence"
>       }
>
> and if I try to edit the config from the browser I see the following:
>
> {
>   "maxFeatureSizeForUnderlyingRefSeq": 250000,
>   "maxFeatureScreenDensity": 100000,
>   "maxHeight": 1000,
>   "style": {
>     "arrowheadClass": null,
>     "className": "{type}",
>     "_defaultHistScale": 4,
>     "_defaultLabelScale": 30,
>     "_defaultDescriptionScale": 120,
>     "minSubfeatureWidth": 1,
>     "maxDescriptionLength": 70,
>     "showLabels": false,
>     "label": "name,id",
>     "description": "note, description",
>     "centerChildrenVertically": false,
>     "renderClassName": null,
>     "subfeatureClasses": {
>       "UTR": "webapollo-UTR",
>       "CDS": "webapollo-CDS",
>       "exon": "container-100pct",
>       "intron": null,
>       "wholeCDS": null,
>       "start_codon": null,
>       "stop_codon": null,
>       "match_part": "darkblue-80pct"
>     },
>     "uniqueIdField": "id"
>   },
>   "hooks": {},
>   "events": {},
>   "menuTemplate": null,
>   "ignoreFeatureFilter": true,
>   "pinned": true,
>   "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
>   "chunkSize": 20000,
>   "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
>   "label": "DNA",
>   "type": "WebApollo/View/Track/AnnotSequenceTrack",
>   "category": "Reference sequence",
>   "key": "Reference sequence",
>   "seqType": "dna",
>   "baseUrl": "http://bf2i300.insa-lyon.fr:8080/apollo/13436489111694940309/jbrowse/data/",
>   "index": 1,
>   "compress": 0,
>   "subfeatures": 1,
>   "metadata": {}
> }
>
> On http://www.yeastgenome.org I saw a different configuration that was displaying both the genome and the six frames which is the following:
>
> {
>   "maxExportSpan": 500000,
>   "showForwardStrand": true,
>   "showReverseStrand": true,
>   "showTranslation": true,
>   "category": "Reference sequence",
>   "type": "JBrowse/View/Track/Sequence",
>   "key": "Reference sequence",
>   "storeClass": "JBrowse/Store/Sequence/StaticChunked",
>   "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
>   "label": "DNA",
>   "chunkSize": 20000,
>   "baseUrl": "http://www.yeastgenome.org/browse/data/",
>   "style": {},
>   "metadata": {}
> }
>
> If I try replacing the configuration on the browser, using the configuration from the yeast and only changing the baseUrl, I do get what I want, but it is not permanent. Therefore I tried replacing the block in the trackList.json file but it seems to override the changes and keeps the same configuration. However, it does seem to be using the trackList.json file because removing a bracket (or breaking the format in any other way) causes the browser to display an error message.
>
> Thank you for your time!
> Carlos
>
> On Fri, Feb 10, 2017 at 6:24 PM, Nathan Dunn <[hidden email]> wrote:
>
> Carlos,
>
> If you update the trackList.json file, those changes should be “permanent”, with the exception that the first time you create an organism it loads all of the sequences into the database for that organism / genome.  
>
> If the changes are significant, for example you changed the genome or sequence names, you’ll likely have to import it as another organism so that it is in-sync.
>
> BTW, what were you changing in the configuration to get it to work?
>
> Nathan
>
>> On Feb 10, 2017, at 8:07 AM, carlos vargas <[hidden email]> wrote:
>>
>> Dear Nathan,
>>
>> I thought this issue could be memory related, but it seems it has to do with the configuration in the trackList.json file. Upon loading webapollo I am still unable to see the reference track, but if I change the configuration (using the edit track configuration option) I am able to see it along with the six frames, however it is only a temporary  solution, for each time I change the page I am using I lose the configuration.
>> I have tried editing the information regarding the Reference sequence track in the trackList.json file, however, when I reload apollo (restarting tomcat) the track configuration is the same as before. Is there a trick to modify the Reference sequence track permenently in the trackList.json file?
>>
>> Thanks for your time,
>> Carlos
>>
>> On Fri, Feb 10, 2017 at 12:03 PM, carlos vargas <[hidden email]> wrote:
>> Dear Nathan,
>>
>> Completely removing all other java versions indeed worked, thanks a lot! However, I am having the same issue I was having with 2.0.2, I am still unable to display the reference sequence (genome and aminoacids on six frames). On switching to a new region they appear as a flash but then they just appear as a "loading" message. I think this is totally unrelated, want me to start a new message thread?
>>
>> Thanks a lot!
>> Carlos
>>
>> On Fri, Feb 10, 2017 at 2:34 AM, Nathan Dunn <[hidden email]> wrote:
>>
>> Carlos,
>>
>>> Unsupported major.minor version 52.0
>>
>> This typically means that the tomcat version you are runnings is probably running Java 7, but we have forced you to install Java / JDK 8 to compile and run.
>>
>> A couple things you can do:
>>
>> - remove java 7 (unless you need it)
>> - in your environment set     JAVA_HOME to the Java 8 JDK (not the JRE) e.g., on Ubuntu . .    JAVA_HOME/usr/lib/jvm/java-8-openjdk-amd64
>>
>> That should do the trick (knock on wood).  
>>
>> Either way, I’ll update the docs to clarify both of these as both of these issues have come up before.
>>
>> Thanks,
>>
>> Nathan
>>
>>> On Feb 9, 2017, at 4:34 PM, carlos vargas <[hidden email]> wrote:
>>>
>>> Dear Nathan,
>>>
>>> I followed your suggestions and updated the groovy file and rebuilt the .war file. I removed both .war files and directories from the webapps folder and then placed the newly made apollo.war file. It was uncompressed but still it gives the same 404 error. The last lines from the catalina output are the following:
>>>
>>>
>>> NFO: Starting Servlet Engine: Apache Tomcat/7.0.28
>>> Feb 10, 2017 1:18:08 AM org.apache.catalina.startup.HostConfig deployWAR
>>> INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
>>> log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
>>> log4j:WARN Please initialize the log4j system properly.
>>> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
>>> Feb 10, 2017 1:18:14 AM org.apache.catalina.core.ApplicationContext log
>>> INFO: Initializing Spring root WebApplicationContext
>>> 2017-02-10 01:18:22,259 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
>>> org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> 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:745)
>>> Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
>>> at java.lang.Class.getDeclaredFields(Class.java:1819)
>>> ... 5 more
>>> 2017-02-10 01:18:22,261 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> 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:745)
>>> Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
>>> at java.lang.Class.getDeclaredFields(Class.java:1819)
>>> ... 5 more
>>> 2017-02-10 01:18:22,262 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> 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:745)
>>> Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
>>> at java.lang.Class.getDeclaredFields(Class.java:1819)
>>> ... 5 more
>>> Feb 10, 2017 1:18:22 AM 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 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> 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:745)
>>> Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
>>> at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
>>> at java.lang.Class.getDeclaredFields(Class.java:1819)
>>> ... 5 more
>>>
>>> Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
>>> SEVERE: Error listenerStart
>>> Feb 10, 2017 1:18:22 AM org.apache.catalina.core.StandardContext startInternal
>>> SEVERE: Context [/apollo] startup failed due to previous errors
>>> Feb 10, 2017 1:18:22 AM org.apache.catalina.startup.HostConfig deployDirectory
>>> INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
>>> Feb 10, 2017 1:18:23 AM org.apache.coyote.AbstractProtocol start
>>> INFO: Starting ProtocolHandler ["http-bio-8080"]
>>> Feb 10, 2017 1:18:23 AM org.apache.catalina.startup.Catalina start
>>> INFO: Server startup in 15218 ms
>>>
>>> Thank you!
>>> Carlos
>>>
>>>
>>> On Thu, Feb 9, 2017 at 10:51 PM, Nathan Dunn <[hidden email]> wrote:
>>>
>>> Carlos,
>>>
>>> If they are both pointing to the SAME database, but with different versions of the software, you are likely going to have problems with one or both instances.
>>>
>>> However, if “/apollo” is the new version and it seems to be working and “/test” is the old version and it isn’t, that is good.   I would shut down the tomcat server and remove the “test.war” and directory code either way as it can only cause errors.  However, if they are pointing to separate databases they are fine running side by side.  
>>>
>>> If neither version is working then I would:
>>>
>>> - recreate your old database from the backup you made (hopefully)
>>> - load ONLY the newly built tomcat as a war file
>>>
>>> The new code will attempt to update the server.
>>>
>>> If for some reason it still isn’t working then update the apollo-config.groovy file you are using with a log4j entry with something like this:
>>>
>>> http://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=log4j#logging-configuration
>>>
>>> log4j
>>> .main = {
>>>     error 'org.codehaus.groovy.grails.we
>>> b.servlet',  // controllers
>>>           'org.codehaus.groovy.grails.we
>>> b.pages',    // GSP
>>>           'org.codehaus.groovy.grails.we
>>> b.sitemesh', // layouts
>>>     debug ‘grails.app’
>>>
>>> }
>>> and redump the catalina.out
>>>
>>> Nathan
>>>
>>>> On Feb 9, 2017, at 1:18 PM, carlos vargas <[hidden email]> wrote:
>>>>
>>>> Dear Nathan,
>>>>
>>>> Thank you very much for your prompt reply! Indeed the webapp directory does look like that. I used almost the same old apollo-config.groovy file, I just had to comment the jbrowse lines because it was unable to find them in the same paths as were set in the old file, but apart from that I changed nothing. I did download the tar.gz file from the release page, and finally regarding the tomcatlogs I get the following messages (it might seem contradictory, but apollo.war is the new version and test.war is the old version).
>>>>
>>>> INFO: Starting service Catalina
>>>> Feb 09, 2017 7:33:54 PM org.apache.catalina.core.StandardEngine startInternal
>>>> INFO: Starting Servlet Engine: Apache Tomcat/7.0.28
>>>> Feb 09, 2017 7:33:54 PM org.apache.catalina.startup.HostConfig deployWAR
>>>> INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
>>>> Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
>>>> INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
>>>> Feb 09, 2017 7:34:00 PM org.apache.catalina.startup.TaglibUriRule body
>>>> INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
>>>> Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
>>>> SEVERE: Error listenerStart
>>>> Feb 09, 2017 7:34:08 PM org.apache.catalina.core.StandardContext startInternal
>>>> SEVERE: Context [/apollo] startup failed due to previous errors
>>>> Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.HostConfig deployDirectory
>>>> INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
>>>> Feb 09, 2017 7:34:08 PM org.apache.coyote.AbstractProtocol start
>>>> INFO: Starting ProtocolHandler ["http-bio-8080"]
>>>> Feb 09, 2017 7:34:08 PM org.apache.catalina.startup.Catalina start
>>>> INFO: Server startup in 14376 ms
>>>> Feb 09, 2017 7:35:58 PM org.apache.catalina.startup.HostConfig deployWAR
>>>> INFO: Deploying web application archive /var/lib/tomcat7/webapps/test.war
>>>> Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
>>>> INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
>>>> Feb 09, 2017 7:36:03 PM org.apache.catalina.startup.TaglibUriRule body
>>>> INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
>>>>
>>>>
>>>> Thanks a lot!
>>>> Carlos
>>>>
>>>> On Thu, Feb 9, 2017 at 9:40 PM, Nathan Dunn <[hidden email]> wrote:
>>>>
>>>> Carlos,
>>>>
>>>> To clarify a few things:
>>>>
>>>> 1 - Your webapp directory looks roughly like this (where apollo202 is your older URL and test is your 2.0.5 installation) : apollo202.war apollo202/  test.war test/   ?
>>>>
>>>> 2 - You built test.war with the same apollo-config.groovy file you used for your older installation?
>>>>
>>>> 3 - If you updated in place (off of GitHub) you should have done an “./apollo clean-all”, i you built from the “release” page source on GitHub (recommended), this won’t matter as the source is already clean.  It sounded like you downloaded from the “release” page.
>>>>
>>>> 4 - What do your tomcat logs look like (often in a file called catalina.out)?
>>>>
>>>> Thanks,
>>>>
>>>> Nathan
>>>>
>>>>> On Feb 9, 2017, at 10:47 AM, carlos vargas <[hidden email]> wrote:
>>>>>
>>>>> Hello everyone,
>>>>>
>>>>> I have been using webapollo 2.0.2 for a couple of months, but I have been having trouble displaying the genome and coding frames, therefore I tried updating to version 2.0.6.
>>>>> I followed the instructions in http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production and successfully generated the war file. However, on moving it to webapps I am unable to launch the application. While restarting tomcat the war file is uncompressed and the folder is generated, but it displays a 404 error (The requested resource (/test) is not available) while trying to access it.
>>>>> I renamed the old installation and i am still able to access it (changing the url accordingly). Do you have any ideas as to what might be the problem? Thanks a lot!
>>>>>
>>>>> Best,
>>>>> Carlos
>>>>>
>>>>>
>>>>>
>>>>> 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>>
>
>
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>
>
> 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 [hidden email] | 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 [hidden email] | 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 [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.