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.

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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2010-2020, The Open Microscopy Environment