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IDR / idr-utils

Utility scripts for managing IDR submissions
BSD 2-Clause "Simplified" License
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Add swap_filesets.py #53

Open will-moore opened 1 year ago

will-moore commented 1 year ago

Adds the swap_filesets.py script developed as part of the workflow at https://github.com/IDR/idr-metadata/issues/652

e.g.

$ python swap_filesets.py Fileset:1 Fileset:2
$ python swap_filesets.py Image:1 Image:2 --report --dry-run

# gets the Fileset from first image in each Plate. Swaps all images in each Fileset
$ python swap_filesets.py Plate:1 Plate:2 --report --dry-run

# matches Plates by name
$ python swap_filesets.py Screen:1 Screen:2

This will also print an psql command that is needed to update the original Fileset:1 to reference the key file of Fileset:2 which is assumed to be NGFF data.

will-moore commented 1 year ago

As discussed today in IDR meeting: we may not want to delete the old Filesets as part of the NGFF conversion workflow. We can leave them "orphaned" with no Images as a record of the previous state of the server. Could possibly use details.externalInfo as a way to store the previous Fileset ID on each Image.

will-moore commented 1 year ago

I found https://docs.openmicroscopy.org/omero-blitz/5.5.8/javadoc/omero/model/ExternalInfo.html on ExternalInfo but no idea what the fields mean or how to store an arbitrary number there. This is being used by Glencoe? cc @sbesson