Part IV. Developer documentation

Table of Contents

24. Migrating code from BASE 2 to BASE 3

24.1. Compiling the code against BASE 3

24.2. Core API changes

24.3. Packaging your plug-in so that it installs in BASE 3

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. The Extensions API

25.8. Plug-ins

25.9. Client applications

26. Plug-in developer

26.1. How to organize your plug-in project

26.1.1. Using Ant

Directory and file layout

The build file

Building the plug-in

26.1.2. Make the plug-in compatible with the auto-installation wizard

Installing plug-in configurations

26.2. The Plug-in API

26.2.1. The main plug-in interfaces

The net.sf.basedb.core.plugin.Plugin interface

The net.sf.basedb.core.plugin.InteractivePlugin interface

26.2.2. How the BASE core interacts with the plug-in when...

Installing a plug-in

Configuring a plug-in

Checking if a plug-in can be used in a given context

Creating a new job

Executing a job

26.2.3. Abort a running a plug-in

26.2.4. Using custom JSP pages for parameter input

26.3. Import plug-ins

26.3.1. Autodetect file formats

The net.sf.basedb.core.plugin.AutoDetectingImporter interface

Call sequence during autodetection

26.3.2. The AbstractFlatFileImporter superclass

Configure by example

26.4. Export plug-ins

26.4.1. Immediate download of exported data

The ImmediateDownloadExporter interface

The ExportOutputStream class

Call sequence during immediate download

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. File unpacker plug-ins

26.6.2. File packer plug-ins

26.7. How BASE load plug-in classes

26.8. 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

27.2.1. The extensions.xml file

27.2.2. Extending multiple extension points with a single 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

27.6.1. Error handlers

27.7. Custom servlets

27.8. Extension points defined by BASE

27.8.1. Menu: extensions

27.8.2. Toolbars

27.8.3. Edit dialogs

27.8.4. Bioassay set: Tools

27.8.5. Bioassay set: Overview plots

27.8.6. Services

27.8.7. Service actions

27.8.8. Connection managers

27.8.9. Fileset validators

27.8.10. Logging managers

The LogManagerFactory interface

The LogManager interface

The EntityLogger interface

27.8.11. Item overview loaders

27.8.12. Item overview validation

27.8.13. Item overview information

27.8.14. Table list columns

27.8.15. Query filters

27.8.16. Login manager

Supporting multiple installed login managers

Internal vs. external authentation

Configuration settings

27.8.17. Login form

The before-login event

27.8.18. Skins

27.8.19. Start page

28. Web services

29. The BASE API

29.1. The Public API of BASE

29.1.1. What is backwards compatibility?

Binary compatibility

Contract compatibility

Source code compatibility

29.2. The Data Layer API

29.2.1. Basic classes and interfaces

Classes

Interfaces

29.2.2. User authentication and access control

Users and passwords

Groups, roles, projects and permission template

Keys

Permissions

29.2.3. Reporters

Reporters

Reporter lists

29.2.4. Quota and disk usage

Quota

Disk usage

29.2.5. Client, session and settings

Clients

Sessions

Settings

29.2.6. Files and directories

29.2.7. Experimental platforms and item subtypes

Platforms

Item subtypes

FileStoreEnabled items and data files

29.2.8. Parameters

29.2.9. Annotations

Annotations

Annotation types

Units

Categories

29.2.10. Protocols, hardware and software

Protocols

Parameters

Hardware and software

29.2.11. Plug-ins, jobs and job agents

Plug-ins

Jobs

Job agents

29.2.12. Biomaterial LIMS

Biomaterials

Bioplates and plate types

Biomaterial and plate events

29.2.13. Array LIMS - plates

Plates

Plate events

Plate mappings

29.2.14. Array LIMS - arrays

Array designs

Array slides

29.2.15. Bioassays and raw data

Physical bioassays

Raw data

29.2.16. Experiments and analysis

Experiments

Bioassay sets, bioassays and transformations

Virtual databases, datacubes, etc.

The dynamic database

29.2.17. Other classes

29.3. The Core API

29.3.1. Authentication and sessions

29.3.2. Access permissions

29.3.3. Data validation

29.3.4. Transaction handling

29.3.5. Create/read/write/delete operations

29.3.6. Batch operations

29.3.7. Quota

29.3.8. Plugin execution / job queue

29.3.9. Using files to store data

Diagram of classes and methods

Use case: Asking the user for files for a given item

Use case: Link, validate and extract metadata from the selected files

Use case: Import data into the database

Use case: Using raw data from files in an experiment

29.3.10. Sending signals (to plug-ins)

Diagram of classes and methods

29.4. The Query API

29.5. The Dynamic API

29.6. The 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

Organization of source files

Create new chapter/file

Controlling chunking

The id attribute

Help text for the BASE web client

Build the documentation

30.1.3. Docbook tags to use

Text elements

Code elements

Gui elements

Images and figures

Examples and program listing

Admonitions

Lists

Link elements

30.2. Create UML diagrams with MagicDraw

30.2.1. Organisation

30.2.2. Classes

Data layer classes

Core layer classes

30.2.3. Diagrams

Create a new diagram

Visual appearance and style

Save diagram as image

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

Naming

Layout and comments

Statements

31.3.3. API changes and backwards compatibility

31.3.4. Data-layer rules

31.3.5. Item-class rules

Basic class and interface hierarchy

Access permissions

Data validation

Participating in transactions

Template code for item classes

31.3.6. Batch-class rules

31.3.7. Test-class rules