Table of Contents

29.1. The Public API of BASE

29.1.1. What is backwards compatibility?

Binary compatibility

Contract compatibility

Source code compatibility

29.2. The database schema and the Data Layer API

29.2.1. Basic classes and interfaces

UML diagram

Classes

Interfaces

29.2.2. User authentication and access control

UML diagram

Users and passwords

Groups, roles, projects and permission template

Keys

Permissions

29.2.3. Hardware and software

UML diagram

Hardware and software

29.2.4. Reporters

UML diagram

Reporters

Reporter lists

29.2.5. Quota and disk usage

UML diagram

Quota

Disk usage

29.2.6. Client, session and settings

UML diagram

Clients

Sessions

Settings

29.2.7. Files and directories

UML diagram

Description

29.2.8. Experimental platforms

UML diagram

Platforms

FileStoreEnabled items and data files

29.2.9. Parameters

UML diagram

Parameters

29.2.10. Annotations

UML diagram

Annotations

Annotation types

Units

Categories

29.2.11. Protocols

UML diagram

Protocols

Parameters

29.2.12. Plug-ins, jobs and job agents

UML diagram

Plug-ins

Jobs

Job agents

29.2.13. Biomaterial LIMS

UML diagram

Biomaterial LIMS

Bioplates and plate types

Biomaterial and plate events

29.2.14. Array LIMS - plates

UML diagram

Plates

Plate events

Plate mappings

29.2.15. Array LIMS - arrays

UML diagram

Array designs

Array slides

29.2.16. Hybridizations and raw data

UML diagram

Hybridizations

Raw data

Spot images

29.2.17. Experiments and analysis

UML diagram

Experiments

Bioassay sets, bioassays and transformations

Virtual databases, datacubes, etc.

The dynamic database

29.2.18. Other classes

UML diagram

29.3. The Core API

29.3.1. 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

29.3.2. Sending signals (to plug-ins)

Diagram of classes and methods

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