[ome-devel] Versioning objects e.g. features in OMERO

[Simon Li]

Hi all

I've been working with Chris Coletta on getting the latest version of WND-CHARM to work with OMERO, and I've stumbled into the problem of how to version objects such as calculated features in OMERO. I thought this might be relevant for others on the list, and also ties in with the ongoing OMERO.features discussion.

Example use cases:

1. I've calculated and stored some features with v1.5 of WND-CHARM. Later I upgrade WND-CHARM to v2.0. How do I know that my v1.5 features may need to be either converted or re-calculated to v2.0. Similarly for a trained classifier.

2. I've upgraded WND-CHARM. Can I run a script which finds all WND-CHARM 1.5 objects and converts them into v2.0 format?

We might also want to think about versioning the same object from a user's perspective, e.g. if they redo their analysis with different parameters and save it into OMERO they might want to keep their previous versions.

A few initial ideas:
* Namespace. Annotations in OMERO have a namespace (string) field, e.g. If the WND-CHARM  results are stored in a file attached to an OMERO object this will be in the form of a FileAnnotation, so the version could be incorporated, e.g.:

    namespace=/Classifer/WndCharm/1.5

* TextAnnotation. Can be added to anything, and could be used as a key-value pair. Note this differs from the previous in that the TextAnnotation is a completely separate object which is linked to the saved WND-CHARM object:

    namespace=/Classifer/WndCharm/Version
    value=1.5

* Key-Value pairs in OMERO. This work is currently ongoing.

Thinking further ahead Gianluigi Zanetti's group have been working on bringing a graph database into OMERO [1], which would allow us to store the full history of all calculations (source data, all transformations, parameters, multiple runs, etc).

Cheers

Simon

[1] https://www.openmicroscopy.org/site/support/partner/omero.biobank/





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