OMERO Core Scripts
This directory contains OMERO scripts which use the OMERO.scripts API. All scripts (e.g. *.py) present in the directory will be automatically distributed with all binary builds. Which file-endings will be detected and how they will be launched are both configured centrally in the server. .py, .jy", and ``.m (MATLAB) files should all be detected by default starting with OMERO 5.
Scripts are separated into several categories, one per directory.
Scripts which would like to rely on other scripts can use:
For this to work, the official script in question must be properly importable, i.e.:
- def run():
- client = omero.scripts.client(…)
- if __name__ == “__main__”:
OMERO User Scripts
If you would like to provide your own scripts for others to install into their OMERO installations, please see http://openmicroscopy.org/info/scripts
Integration tests under test/ require an OMERO server with scripts installed. The tests are run by Travis for open PRs using omero-test-infra to deploy OMERO via Docker containers.
To run tests locally:
# All tests $ python setup.py test
# Single test in a single file $ python setup.py test -t test/integration/test_util_scripts.py -k test_dataset_to_plate
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