LabKey Server Module Development

When working on LabKey Server modules, consult these documentation files.

Core Files

1. •ai/docs/labkey/testresults-module.md - Architecture of the testresults module (controller, schema, JSP views, model classes)
2. •ai/docs/labkey-dev-setup.md - LabKey development environment setup

Skyline Team LabKey Modules

All MacCossLab LabKey modules live under:

labkeyEnlistment/server/modules/MacCossLabModules/

Key Modules

• •targetedms - The Panorama module. Our most important LabKey module overall. Stores and visualizes targeted mass spec data. Started by Vagisha, now largely maintained by LabKey with funding from pharma contracts. Foundation of the entire Panorama platform.
• •panoramapublic - Panorama Public, our public-facing repository for publishable proteomics data as part of ProteomeXchange. Maintained by Vagisha. High external visibility.
• •pwebdashboard - Panorama web dashboard. Maintained by Vagisha.
• •testresults - Nightly test results dashboard on skyline.ms. Internal to the Skyline team but critical for development workflow. Primary data source for the LabKey MCP server that supports our /pw-daily reporting system.

Build Commands

# Build and deploy the testresults module
cd C:/proj/labkeyEnlistment
gradlew :server:modules:MacCossLabModules:testresults:deployModule

Key Patterns

• •Controllers extend SpringActionController with static inner action classes
• •Actions use @RequiresPermission, @RequiresSiteAdmin, or @RequiresNoPermission
• •API actions extend MutatingApiAction or ReadOnlyApiAction and return ApiSimpleResponse
• •Views are JSP files under the module's view/ directory
• •SQL uses SQLFragment with parameterized queries (never string concatenation for values)
• •Transactions use DbScope.Transaction with try-with-resources
• •Schema access goes through static methods on the module's schema class (e.g., TestResultsSchema.getTableInfoTestRuns())
• •CSRF - JSP forms use LABKEY.CSRF header for POST requests
• •JSP URL generation uses jsURL(new ActionURL(...)) for JavaScript and h(new ActionURL(...)) for HTML attributes