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:
$ omero mkngff sql --symlink_repo /OMERO/ManagedRepository --secret=secret 1234 /path/to/fileset.zarr > myNgff.sql $ psql -U omero -d idr -h $DBHOST -f myNgff.sql
To ONLY perform the symlink creation:
$ omero mkngff symlink /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
2017-2020, The Open Microscopy Environment