omero-mkngff

Plugin to swap OMERO filesets with NGFF

Usage

To create sql containing required functions and run it:

$ omero mkngff setup > setup.sql
$ psql -U omero -d idr -h $DBHOST -f setup.sql

To generate sql and create the symlinks from the ManagedRepository to the NGFF data for a specified Fileset ID: The clientpath is used as the basis for the clientpath for each file in the Fileset. If omitted then the clientpath is 'unknown'. When writing .zarr.bfoptions into the ManagedRepository alongside the symlink to fileset.zarr, the clientpath will be added to bfoptions as omezarr.alt_store, allowing ZarrReader to read directly from that source.

$ omero mkngff sql --symlink_repo /OMERO/ManagedRepository --secret=secret --bfoptions --clientpath=https://url/to/fileset.zarr 1234 /path/to/fileset.zarr > myNgff.sql
$ psql -U omero -d idr -h $DBHOST -f myNgff.sql

To ONLY perform the symlink creation (and optionally create fileset.zarr.bfoptions with clientpath as above)

$ omero mkngff symlink /OMERO/ManagedRepository 1234 /path/to/fileset.zarr --bfoptions --clientpath=https://url/to/fileset.zarr

To ONLY create fileset.zarr.bfoptions

$ omero mkngff bfoptions /OMERO/ManagedRepository 1234 /path/to/fileset.zarr

Requirements

• OMERO 5.6.0 or newer
• Python 3.6 or newer

Installing from PyPI

This section assumes that an OMERO.py is already installed.

Install the command-line tool using pip:

$ pip install -U omero-mkngff

Release process

This repository uses bump2version to manage version numbers. To tag a release run:

$ bumpversion release

This will remove the .dev0 suffix from the current version, commit, and tag the release.

To switch back to a development version run:

$ bumpversion --no-tag [major|minor|patch]

specifying major, minor or patch depending on whether the development branch will be a major, minor or patch release. This will also add the .dev0 suffix.

Remember to git push all commits and tags.

License

This project, similar to many Open Microscopy Environment (OME) projects, is licensed under the terms of the GNU General Public License (GPL) v2 or later.

Copyright

2023-2024, The Open Microscopy Environment