design-principles.md

Design Principles

The following conventions describe the Python implementation. Matlab conventions are similar and will be described separately.

DataJoint Schemas

DataJoint allows creating database schemas, which are namespaces for collections of related tables.

The following commands declare a new schema and create the object named schema to reference the database schema.

import datajoint as dj
schema = dj.schema('<schema_name>')

We follow the convention of having only one schema defined per Python module. Then such a module becomes a "DataJoint schema" comprising a python module with a corresponding database schema.

The module's schema object is then used as the decorator for classes that define tables in the database.

Elements

An Element is a software package defining one or more DataJoint schemas serving a particular purpose. By convention, such packages are hosted in individual GitHub repositories. For example, Element element_calcium_imaging is hosted at https://github.com/datajoint/element-calcium-imaging, and contains two DataJoint schemas: scan and imaging.

Deferred schemas

A deferred schema is one in which the name of the database schema name is not specified. This module does not declare schema and tables upon import. Instead, they are declared by calling schema.activate('<schema_name>') after import.

By convention, all modules corresponding to deferred schema must declare the function activate which in turn calls schema.activate.

Thus Element modules begin with

import datajoint as dj
schema = dj.schema()

def activate(schema_name):
	schema.activate(schema_name)

However, many activate functions perform other work associated with activating the schema such as activating other schemas upstream.

Linking Module

To make the code more modular with fewer dependencies, Elements' modules do not import upstream schemas directly. Instead, all required classes and functions must be defined in a linking_module and passed to the module's activate function.

For instance, the element_calcium_imaging.scan module receives its required functions from the linking module passed into the module's activate function. See the corresponding workflow for an example of how the linking module is passed into the Element's module.