[apollo] Ref Sequence issue & more

Nathan Dunn

2016-07-14 19:14:35 UTC

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):

https://github.com/GMOD/Apollo/archive/2.0.3.zip <https://github.com/GMOD/Apollo/archive/2.0.3.zip>

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

http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production <http://genomearchitect.readthedocs.io/en/stable/Migration.html#migration-from-2-0-x-to-2-0-y-on-production>

In theory the database will update itself automatically when you do the upgrade, but we donât 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

Post by 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.
Version: 2.0.2-RC2-SNAPSHOT <https://github.com/GMOD/Apollo/releases>
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 <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 <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 <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 <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 <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 <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/