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. Categories ---------- Scripts are separated into several categories, one per directory. | In the directory | should be scripts which ... | | ---------------- | --------------------- | | **analysis_scripts** | crunch images to produce numerical results and similar tasks | | **export_scripts** | take one or more images as an input, and produce a representation for exchange| | **figure_scripts** | take one or more images as an input, and produce a summary representation | | **hcs_scripts** | work with screens/plates/wells rather than just images | | **import_scripts** | are run on images after import for extra processing | | **processing_scripts** | create new images from existing images or other data | | **setup_scripts** | are executed once, often by administrators, to configure OMERO itself | | **util_scripts** | perform other miscellaneous tasks like cleaning up or optimizing OMERO itself | Scripts which would like to rely on other scripts can use: import omero.<sub_dir>.<script_name> For this to work, the official script in question must be properly importable, i.e.: def run(): client = omero.scripts.client(...) if __name__ == "__main__": run() 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 Testing ------- 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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