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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.
dj.createSchema simplifies the process, the manual approach yields a better understanding of what actually takes place, so both approaches are listed below.
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
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
For example, for the schema called
experiment, you would create the folder
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
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.
+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.
Alternatively, you can execute
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.