Part IV. Developer documentation
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Part IV. Developer documentation
Table of Contents
25. Developer overview of BASE
25.1. Fixed vs. dynamic database
25.2. Hibernate and the DbEngine
25.3. The Batch API
25.4. Data classes vs. item classes
25.5. The Query API
25.6. The Controller API
25.7. Plug-ins
25.8. Client applications
26. Plug-in developer
26.1. How to organize your plug-in project
26.1.1. Using Ant
26.1.2. With Eclipse
26.1.3. Make the plug-in compatible with the auto-installation wizard
26.2. The Plug-in API
26.2.1. The main plug-in interfaces
26.2.2. How the BASE core interacts with the plug-in when...
26.2.3. Using custom JSP pages for parameter input
26.3. Import plug-ins
26.3.1. Autodetect file formats
26.3.2. The AbstractFlatFileImporter superclass
26.4. Export plug-ins
26.4.1. Immediate download of exported data
26.4.2. The AbstractExporterPlugin class
26.5. Analysis plug-ins
26.5.1. The AbstractAnalysisPlugin class
26.5.2. The AnalysisFilterPlugin interface
26.6. Other plug-ins
26.6.1. Authentication plug-ins
26.6.2. Secondary file storage plugins
26.6.3. File unpacker plug-ins
26.6.4. File packer plug-ins
26.6.5. File validator and metadata reader plug-ins
26.7. Enable support for aborting a running a plug-in
26.8. How BASE load plug-in classes
26.9. Example plug-ins (with download)
27. Extensions developer
27.1. Overview
27.1.1. Download code examples
27.1.2. Terminology
27.2. Hello world as an extension
27.3. Custom action factories
27.4. Custom images, JSP files, and other resources
27.4.1. Javascript and stylesheets
27.4.2. X-JSP files
27.5. Custom renderers and renderer factories
27.6. Extension points
27.7. Custom servlets
28. Web services
28.1. Available services
28.1.1. Services
28.2. Client development
28.2.1. Receiving files
28.3. Services development
28.3.1. Generate WSDL-files
28.4. Example web service client (with download)
29. API overview (how to use and code examples)
29.1. The Public API of BASE
29.1.1. What is backwards compatibility?
29.2. The database schema and the Data Layer API
29.2.1. Basic classes and interfaces
29.2.2. User authentication and access control
29.2.3. Hardware and software
29.2.4. Reporters
29.2.5. Quota and disk usage
29.2.6. Client, session and settings
29.2.7. Files and directories
29.2.8. Experimental platforms
29.2.9. Parameters
29.2.10. Annotations
29.2.11. Protocols
29.2.12. Plug-ins, jobs and job agents
29.2.13. Biomaterials
29.2.14. Array LIMS - plates
29.2.15. Array LIMS - arrays
29.2.16. Hybridizations and raw data
29.2.17. Experiments and analysis
29.2.18. Other classes
29.3. The Core API
29.3.1. Using files to store data
29.3.2. Sending signals (to plug-ins)
29.4. The Query API
29.5. Analysis and the Dynamic and Batch API:s
29.6. Extensions API
29.6.1. The core part
29.6.2. The web client part
29.7. Other useful classes and methods
30. Write documentation
30.1. User, administrator and developer documentation with Docbook
30.1.1. Documentation layout
30.1.2. Getting started
30.1.3. Docbook tags to use
30.2. Create UML diagrams with MagicDraw
30.2.1. Organisation
30.2.2. Classes
30.2.3. Diagrams
30.3. Javadoc
30.3.1. Writing Javadoc
31. Core developer reference
31.1. Publishing a new release
31.2. Subversion / building BASE
31.3. Coding rules and guidelines
31.3.1. Development process and other important procedures
31.3.2. General coding style guidelines
31.3.3. API changes and backwards compatibility
31.3.4. Data-layer rules
31.3.5. Item-class rules
31.3.6. Batch-class rules
31.3.7. Test-class rules
31.4. Internals of the Core API
31.4.1. Authentication and sessions
31.4.2. Access permissions
31.4.3. Data validation
31.4.4. Transaction handling
31.4.5. Create/read/write/delete operations
31.4.6. Batch operations
31.4.7. Quota
31.4.8. Plugin execution / job queue