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OMERO CLI upload

Plugin for uploading files using the OMERO Command Line Interface (CLI).

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-upload

Usage

The plugin is called from the command-line using the omero command.

To upload a single file:

$ omero upload <file>

This command will create an OriginalFile on the server and return an output of type OriginalFile:<id>.

To upload multiple files:

$ omero upload <file1> <file2>

This command will create two OriginalFile and return an output of type OriginalFile:<id1>,<id2>

By default, the mimetype will be guessed from the filename but it can be specified by using the --mimetype argument:

$ omero upload <file1> --mimetype 'test/csv'

Files can be in-place uploaded into the OMERO.server via symlinked rather than being copied. This requires the command to be run on the OMERO.server itself from a user having write permissions to the OMERO data repository, similarly to the [in-place import](https://docs.openmicroscopy.org/omero/latest/sysadmins/in-place-import.html). To run an in-place upload, the --data-dir argument must be passed to specify the binary OMERO directory:

$ omero upload <file1> --data-dir /OMERO

Instead of creating and returning a simple OriginalFile object, it is also possible to wrap the file within a FileAnnotation which can then be linked to other objects in the database. It is possible to specify the namespace of this FileAnnotation using the --namespace argument:

$ omero upload <file1> --wrap --namespace 'openmicroscopy.org/idr/analysis/original'

This command will create an OriginalFile and a FileAnnotation and return an output of type FileAnnotation:<id>.

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

2019-2020, The Open Microscopy Environment