Commits

Author Commit Message Labels Comments Date
Jochen Schramm
Add missing template
Jochen Schramm
The function to display the model nav bar correctly
Jochen Schramm
Placeholders for 2 rules and new event rule As they are not working by now the calls of rate rules and assignment rules are replaced by dummy text. The functionality is left there as it may be useful when the rules work again. Event assignment is added but as well with dummy text.
Mihai Glonț
Updated to JSBML 1.0. Published a jar containing a snapshot of the JSBML trunk on http://www.ebi.ac.uk/~maven/m2repo_snapshots/org/sbml/jsbml/jsbml/1.0-SNAPSHOT/ and updated our dependencies. Removed the jsbml0.8 and biojava1.7 jars from pluginlibs/ as they are no longer required.
Mihai Glonț
Investigating Weceem and Quartz. We now know what causes the memory leaks: it's the weceem jobs. More exactly, Weceem starts the Quartz scheduler, launches jobs, but it doesn't wait for them to complete before the scheduler is closed, so you end up with quartzScheduler threads lurking around. Temporary fix: wait a bit in the destroy() method :) Better fix: patch the way in which the QuartzConfig settings are applied in QuartzGra…
Mihai Glonț
Resolved dependency conflicts. TODO: Get rid of the transitive dependency of hibernate on slf4j-api version 1.6.2
Mihai Glonț
Update Hibernate 3.6 property. In Hibernate 3.6 the property cache.provider_class was replaced by cache.region.factory_class as per http://ehcache.org/documentation/integrations/hibernate#hibernate-33-and-higher
Mihai Glonț
Fixed the way the Weceem security policy gets loaded. Dashes are not allowed in Groovy class identifiers, hence the policy script has been renamed to WeceemSecurity.groovy. In order to specify the location of this security policy, one can either set the property jummp.security.cms.policy in .jummp.properties or via the environment variable JUMMP_SECURITY_CMS_POLICY. If neither are used, the Weceem default permissions are used: create, read, updat…
Mihai Glonț
Added IntelliJ IDEA project files to gitignore
Mihai Glonț
Web application is now an inline plugin.
Mihai Glonț
Disabled JMS and Quartz to prevent memory leaks when JUMMP is stopped in Tomcat. Commented out the AuthenticationOutdaterJob job as it relied on Quartz. We should re-implement the functionality differently. Our previous Weceem security policy, stored in scripts/weceem-security.groovy, threw ClassFormatErrors. For now, use the default wcm security policy. Weceem lists Quartz 0.4.2 as a dependency and uses it internally. Be sure to edit ~/.grails/$version/jummp/plugins/weceem*/…
Mihai Glonț
Merge with Jochen and Martin. The latest changesets were obtained from the Mercurial repository located at https://bitbucket.org/schrammj/jummp by exporting it to an empty Git repo and then pulling the changes.
Jochen Schramm
Jochen Schramm
Add controller for sbml sbml functionality for new new web interface
Jochen Schramm
Add overview and download
Jochen Schramm
Add model navigation tabs to appear
Jochen Schramm
gsps to display the model
Jochen Schramm
Add sub menu for model A sub menu for the models' detailed information is opened under the normal menu when clicking on the "Model" tab. Additionally, messages are applied.
Jochen Schramm
Correct message
Jochen Schramm
Tags for functioning the web interface The tags here are needed to access the sbml part of the models as they are now implemented in the new web interface.
Jochen Schramm
Additional messages for the model overlay
Jochen Schramm
Adjust login/logout button to content div
Martin Gräßlin
Fix Miriam Controller Incorrect link in admin sidebar and incorrect param passed to update miriam resources.
Mihai Glonț
Fixed the way the build version is generated. The imprint is now obtained from git, not hg.
Mihai Glonț
fixed POSTRGESQL typos
Mihai Glonț
configured exclusions.
Mihai Glonț
excluded version numbers from the name of war files
Martin Gräßlin
Whitelist a false positive JSLint warning
Martin Gräßlin
Fix messy whitespaces JSLint error Now all JS files validate without the messy white spaces option.
Martin Gräßlin
Remove postfix increment from all JS files No idea what is evil about using ++ in for loops, but JSLint does not like it and it's better to not have the check turned off.
  1. Prev
  2. Next