1. Jochen Schramm
  2. jummp

Commits

Author Commit Message Date Builds
Jochen Schramm
Update dependencies As the less CSS plugin got replaced and the new one is used slightly differently 2 gsp pages are also adapted, the main.gsp, and the auth.gsp.
Jochen Schramm
Fix bug preventing communication over dbus The different JUMMP applications communicate via dbus with each other, i.e. JUMMP's core application and the index creator tool. This communication was prevented by a null pointer exception caused by a method call changing a returned config object.
Mihai Glonț
Merged in mgraesslin/jummp/fix-tests (pull request #1)
Martin Gräßlin
Disable JmsAdapterServiceTests Since 4d3c6f7eb5d3273e089015b0502cade6d04f1f6f the JMS plugin is disabled causing all tests of the JmsAdapterServiceTests to fail with a NullPointerException. Disabled for the time being, should be enabled again once JMS plugin is enabled again.
Martin Gräßlin
Adjust SbmlServiceTests to changes in latest SBML version Since the update of JSBML with 8f99b448c9901dd4555ad955f9227dd02ca1f07f the modelNotes are returned in a different format.
Martin Gräßlin
Explicitly state from where the git Repository should find the git dir Since JUMMP migrated to git the command findGitDir returned the wrong git directory if grails is executed from the working tree. The reason is that findGitDir starts to look for the git directory starting from the directory where the JVM is executed. This of course finds the git directory of the local clone of JUMMP. The result is that neither the unit tests nor run-app can work with the git repo…
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.
  1. Prev
  2. Next