OMERO PyFileSystem2 implementation

A Python filesystem abstraction layer that stores files in OMERO.

Installation

pip install fs-omero-pyfs

Example

import fs
fs_url = 'omero://{username}:{password}@{omerohost}'
root = fs.open_fs(fs_url)

OMERO websockets are supported:

fs_url = 'omero+wss://{username}:{password}@{omerohost}/omero-ws'

Caching is highly recommended. cache_ttl is specified in seconds, 0 disables caching.

fs_url = 'omero://{username}:{password}@{omerohost}?cache_ttl=120'

The OMERO group can be changed by passing a query parameter groupid=1234.

Development notes

Directories are stored as TagAnnotations in a dedicated namespace. Sub-directories are linked by an AnnotationAnnotationLink to the parent directory.

Files are stored as OriginalFiles, linked by an OriginaFileAnnotationLink to the parent directory. The path property of the OriginalFile is ignored, only name is used.