Synchronization between GSCF and modules does not work correctly

A common problem is a timeout from the web container that runs GSCF (e.g. Apache or Tomcat), when a module fetches the sample metadata for a very large study (thousands of samples). If you use e.g. Apache with mod_proxy, this can be solved by increasing the request timeout in the mod_proxy section (last line):

ProxyStatus On
ProxyPreserveHost On
ProxyPass / balancer://sam-cluster/sam-dbnptest/ stickysession=JSESSIONID|jsessionid nofailover=On
ProxyPassReverse / balancer://sam-cluster/sam-dbnptest/
ProxyPassReverseCookiePath /sam-dbnptest /

# Increase the timeout on the proxy, because the synchronization sometimes takes a lot of time
ProxyTimeout 3600

Plugins will not get installed or Webflow Artefacts not found

If many artefacts or plugins are not found, first run grails upgrade (optionally also cleanup your application). That will probably solve most of the problems:

 cd /path/to/gscf
 rm -rf ~/.grails;grails clean;grails upgrade

This also happens when your webflow plugin has another version than the Grails version you are running. You can change the versions in The hibernate, tomcat and webflow plugins should always have exactly the same version number as Grails itself:


"Found two representations of same collection" error

When using the Grails Webflow (or Ajaxflow) and storing domains in the flow scope you might at some point run into the following error:

 "HibernateException: Found two representations of same collection"

It might be that you modified the domain or added children to the domain and stored them earlier in the flow scope. Later on in the flow, Hibernate somehow cannot synchronize the domains correctly. The issue was solved by using the following two lines of code in the step in your flow where you encoutered the HibernateException?:

  def session = sessionFactory.getCurrentSession()

Webflow or other AJAX driven pages do not work (correctly)

You are probably using Firefox and Firebug. There is an unresolved bug in Firefox (see: causing XMLHttpRequest to not work properly when Firebug is logging XMLHttpRequests. Disable the XMLHttpRequests in your firebug console:

The menu dropdown doesn't work and login doesn't function

Check Firebug > Network traffic. Are the jquery Javascript files being found? If not, try reinstalling the jquery plugin. Also, if you have an SVN revision < 1330 and you are using jquery 1.4.4 (January 2011) you might encounter this, see

Logging with 'user' demo account does not work in fresh checkout of GSCF

Grails seems to have compile issues sometimes. Try running 'grails run-app' again.

Error concerning ontoCAT_v0.9.6.1.jar!/ehcache.xml

This is caused by upgrade issues from bgdt 0.0.5 to bgdt 0.0.6. Try removing the .grails/<version>/projects/gscf/plugins/bgdt-* directories with rm -rf. Or just clean up the whole Grails cache with

rm -rf ~/.grails

That approach solves many compilation issues, but it also triggers a lot of re-downloading and re-compiling of course.

Last modified 11 years ago Last modified on Dec 12, 2011, 6:04:09 PM

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