This directory contains the organized documentation for TreeBASE.
- API.md - PhyloWS web service API documentation
- OAI-PMH.md - OAI-PMH metadata harvesting interface documentation
- PAGE_CROSS_REFERENCE.md - Cross-reference of treebase-servlet.xml URL mappings vs v3 user story documentation (identifies pages not yet covered in UI/UX user stories)
Documentation for developers working on TreeBASE:
- BUILDING.md - How to compile and package TreeBASE artifacts
- DEPLOYING.md - How to deploy TreeBASE to a Tomcat server
In-depth technical documentation on specific components and implementations:
- DWR.md - Direct Web Remoting integration and Spring 5 compatibility
- UPGRADES.md - Major dependency and framework upgrades (SLF4J, Jersey, JUnit)
Historical documentation that is no longer relevant for current deployments:
- INSTALL.md - Original data loading environment setup (deprecated)
- LOADING.md - TreeBASE v.1 to v.2 data migration procedures (deprecated)
- Use the PhyloWS API → API.md
- Use the OAI-PMH interface → OAI-PMH.md
- See pages not in user stories → PAGE_CROSS_REFERENCE.md
- Build TreeBASE from source → development/BUILDING.md
- Deploy TreeBASE to a server → development/DEPLOYING.md
- Understand DWR integration → technical-notes/DWR.md
- Learn about recent upgrades → technical-notes/UPGRADES.md
- Find historical data loading info → archive/
When adding new documentation:
- Place development guides in
development/ - Place technical implementation details in
technical-notes/ - Move obsolete documentation to
archive/with a deprecation notice - Update this README with links to new documents
- Update the main README.md if the documentation is widely relevant
- TreeBASE Wiki - High-level documentation
- TreeBASE Website - Public-facing application
- GitHub Issues - Bug reports and feature requests