Creating Schemas

Schemas

On the database server, related tables are grouped into a named collection called a schema. This grouping organizes the data and allows control of user access. A database server may contain multiple schemas each containing a subset of the tables. A single pipeline may comprise multiple schemas. Tables are defined within a schema, so a schema must be created before the creation of any tables.

A schema can be created either automatically using the dj.createSchema script or manually. While dj.createSchema simplifies the process, the manual approach yields a better understanding of what actually takes place, so both approaches are listed below.

Manual

Step 1. Create the database schema

Use the following command to create a new schema on the database server:

query(dj.conn, 'CREATE SCHEMA `alice_experiment`')

Note that you must have create privileges for the schema name pattern (as described in Database Server Hosting). It is a common practice to grant all privileges to users for schemas that begin with the username, in addition to some shared schemas. Thus the user alice would be able to perform any work in any schema that begins with alice_.

Step 2. Create the MATLAB package

DataJoint organizes schemas as MATLAB packages. If you are not familiar with packages, please review:

In your project directory, create the package folder, which must begin with a + sign. For example, for the schema called experiment, you would create the folder +experiment. Make sure that your project directory (the parent directory of your package folder) is added to the MATLAB search path.

Step 3. Associate the package with the database schema

This step tells DataJoint that all classes in the package folder +experiment will work with tables in the database schema alice_experiment. Each package corresponds to exactly one schema. In some special cases, multiple packages may all relate to a single database schema, but in most cases there will be a one-to-one relationship between packages and schemas.

In the +experiment folder, create the file getSchema.m with the following contents:

function obj = getSchema
persistent OBJ
if isempty(OBJ)
    OBJ = dj.Schema(dj.conn, 'experiment', 'alice_experiment');
end
obj = OBJ;
end

This function returns a persistent object of type dj.Schema, establishing the link between the experiment package in MATLAB and the schema alice_experiment on the database server.

Automatic

Alternatively, you can execute

>> dj.createSchema

This automated script will walk you through the steps 1–3 above and will create the schema, the package folder, and the getSchema function in that folder.

Working with existing data

See the chapter Work with Existing Pipelines for how to work with data in existing pipelines, including accessing a pipeline from one language when the pipeline was developed using another.