jaeronga/datajoint-matlab

Relational data pipelines for the science lab

Welcome to DataJoint for MATLAB!

DataJoint for MATLAB is a high-level programming interface for relational databases designed to support data processing chains in science labs. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, and querying data.

For more information, see our general and MATLAB documentation pages.

Citation

• If your work uses DataJoint for MATLAB, please cite the following Research Resource Identifier (RRID) and manuscript.

• DataJoint (RRID:SCR_014543) - DataJoint for MATLAB (version <Enter version number>)

• Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658

For Developers: Running Tests Locally

Click to expand details

• Create an .env with desired development environment values e.g.

MATLAB_USER=rguzman
MATLAB_LICENSE=IyBCRUd... # For image usage instructions see https://github.com/guzman-raphael/matlab, https://hub.docker.com/r/raphaelguzman/matlab
MATLAB_VERSION=R2019a
MATLAB_HOSTID=XX:XX:XX:XX:XX:XX
MATLAB_UID=1000
MATLAB_GID=1000
MYSQL_TAG=5.7
MINIO_VER=RELEASE.2022-01-03T18-22-58Z

• cp local-docker-compose.yaml docker-compose.yaml
• docker-compose up (Note configured JUPYTER_PASSWORD)
• Select a means of running MATLAB e.g. Jupyter Notebook, GUI, or Terminal (see bottom)
• Add tests directory to path e.g. in MATLAB, addpath('tests')
• Run desired tests. Some examples are as follows:

Use Case	MATLAB Code
Run all tests	run(Main)
Run one class of tests	run(TestTls)
Run one specific test	runtests('TestTls/TestTls_testInsecureConn')
Run tests based on test name	import matlab.unittest.TestSuite; import matlab.unittest.selectors.HasName; import matlab.unittest.constraints.ContainsSubstring; suite = TestSuite.fromClass(?Main, ...     HasName(ContainsSubstring('Conn'))); run(suite)

Launch Jupyter Notebook

• Navigate to localhost:8888
• Input Jupyter password
• Launch a notebook i.e. New > MATLAB

Launch MATLAB GUI (supports remote interactive debugger)

• Shell into datajoint-matlab_app_1 i.e. docker exec -it datajoint-matlab_app_1 bash
• Launch Matlab by running command matlab

Launch MATLAB Terminal

• Shell into datajoint-matlab_app_1 i.e. docker exec -it datajoint-matlab_app_1 bash
• Launch Matlab with no GUI by running command matlab -nodisplay