Ref Sequence issue & more

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Ref Sequence issue & more

Shane McCoy
Hello!
I am having an issue of the Reference Sequence not displaying in the JBrowse view when zoomed in. It will stay blank w/ a "Loading" text. I can access the ref seq from the apollo tabs and open. 
My current version:
  • Version: 2.0.2-RC2-SNAPSHOT
  • Grails version: 2.4.5
  • Groovy version: 2.3.11
  • JVM version: 1.7.0_101
I also just saw that version 2.0.3 is out - what is the best course of upgrading to this version? I would like to export annotations to Chado (thanks for adding this!)
Thank you,
Shane McCoy
P.s.
Here is the catalina.out >>

Jul 14, 2016 1:23:24 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'debug' to '0' did not find a matching property.

Jul 14, 2016 1:23:25 PM org.apache.coyote.AbstractProtocol init

INFO: Initializing ProtocolHandler ["http-bio-80"]

Jul 14, 2016 1:23:25 PM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 966 ms

Jul 14, 2016 1:23:25 PM org.apache.catalina.core.StandardService startInternal

INFO: Starting service Catalina

Jul 14, 2016 1:23:25 PM org.apache.catalina.core.StandardEngine startInternal

INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)

Jul 14, 2016 1:23:36 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined

Jul 14, 2016 1:23:36 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined

Jul 14, 2016 1:23:36 PM org.apache.catalina.core.ApplicationContext log

INFO: No Spring WebApplicationInitializer types detected on classpath

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.

Jul 14, 2016 1:23:38 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring root WebApplicationContext


Configuring Shiro ...


Shiro Configured

Jul 14, 2016 1:24:37 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'grails'

Jul 14, 2016 1:24:37 PM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war

Jul 14, 2016 1:24:49 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined

Jul 14, 2016 1:24:49 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined

Jul 14, 2016 1:24:50 PM org.apache.catalina.core.ApplicationContext log

INFO: No Spring WebApplicationInitializer types detected on classpath

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.

Jul 14, 2016 1:24:51 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring root WebApplicationContext


Configuring Shiro ...


Shiro Configured

Jul 14, 2016 1:25:50 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'grails'

Jul 14, 2016 1:25:50 PM org.apache.coyote.AbstractProtocol start

INFO: Starting ProtocolHandler ["http-bio-80"]

Jul 14, 2016 1:25:50 PM org.apache.catalina.connector.MapperListener findDefaultHost

WARNING: Unknown default host [localhost] for connector [Connector[HTTP/1.1-80]]

Jul 14, 2016 1:25:50 PM org.apache.catalina.startup.Catalina start

INFO: Server startup in 145055 ms

Jul 14, 2016 1:25:50 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'gsp'

Jul 14, 2016 1:25:50 PM org.apache.catalina.core.ApplicationContext log

INFO: GSP servlet initialized





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Re: Ref Sequence issue & more

nathandunn

Shane,

For the bug you are encountering, if you have anything in the javascript console, that would be more helpful.  If you know the specific version (the hash from git log), that would also be good as well.  It might be that is already fixed in a newer version. 


You can find 2.0.3 here (or you can upgrade to master in the same way):


We have some very sparse doc for migrating between versions, so let us know if anything is missing:


In theory the database will update itself automatically when you do the upgrade, but we don’t test in-between versions, just on the releases.   Those errors are pretty obvious and we can help you with that.  

Make sure to install node.js and bower to do the build and that if you have grails installed, that you upgrade the version to 2.5.5. 

Nathan

On Jul 14, 2016, at 11:36 AM, Shane McCoy <[hidden email]> wrote:

Hello!
I am having an issue of the Reference Sequence not displaying in the JBrowse view when zoomed in. It will stay blank w/ a "Loading" text. I can access the ref seq from the apollo tabs and open. 
My current version:
  • Version: 2.0.2-RC2-SNAPSHOT
  • Grails version: 2.4.5
  • Groovy version: 2.3.11
  • JVM version: 1.7.0_101
I also just saw that version 2.0.3 is out - what is the best course of upgrading to this version? I would like to export annotations to Chado (thanks for adding this!)
Thank you,
Shane McCoy
P.s.
Here is the catalina.out >>

Jul 14, 2016 1:23:24 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'debug' to '0' did not find a matching property.

Jul 14, 2016 1:23:25 PM org.apache.coyote.AbstractProtocol init

INFO: Initializing ProtocolHandler ["http-bio-80"]

Jul 14, 2016 1:23:25 PM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 966 ms

Jul 14, 2016 1:23:25 PM org.apache.catalina.core.StandardService startInternal

INFO: Starting service Catalina

Jul 14, 2016 1:23:25 PM org.apache.catalina.core.StandardEngine startInternal

INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)

Jul 14, 2016 1:23:36 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined

Jul 14, 2016 1:23:36 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined

Jul 14, 2016 1:23:36 PM org.apache.catalina.core.ApplicationContext log

INFO: No Spring WebApplicationInitializer types detected on classpath

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.

Jul 14, 2016 1:23:38 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring root WebApplicationContext


Configuring Shiro ...


Shiro Configured

Jul 14, 2016 1:24:37 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'grails'

Jul 14, 2016 1:24:37 PM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war

Jul 14, 2016 1:24:49 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined

Jul 14, 2016 1:24:49 PM org.apache.catalina.startup.TaglibUriRule body

INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined

Jul 14, 2016 1:24:50 PM org.apache.catalina.core.ApplicationContext log

INFO: No Spring WebApplicationInitializer types detected on classpath

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.

Jul 14, 2016 1:24:51 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring root WebApplicationContext


Configuring Shiro ...


Shiro Configured

Jul 14, 2016 1:25:50 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'grails'

Jul 14, 2016 1:25:50 PM org.apache.coyote.AbstractProtocol start

INFO: Starting ProtocolHandler ["http-bio-80"]

Jul 14, 2016 1:25:50 PM org.apache.catalina.connector.MapperListener findDefaultHost

WARNING: Unknown default host [localhost] for connector [Connector[HTTP/1.1-80]]

Jul 14, 2016 1:25:50 PM org.apache.catalina.startup.Catalina start

INFO: Server startup in 145055 ms

Jul 14, 2016 1:25:50 PM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'gsp'

Jul 14, 2016 1:25:50 PM org.apache.catalina.core.ApplicationContext log

INFO: GSP servlet initialized




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.