Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add swap_filesets.py #53

Open
wants to merge 7 commits into
base: master
Choose a base branch
from
Open

Conversation

will-moore
Copy link
Member

@will-moore will-moore commented Apr 20, 2023

Adds the swap_filesets.py script developed as part of the workflow at IDR/idr-metadata#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
Copy link
Member Author

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
Copy link
Member Author

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

1 participant