Handle NGFF without OME/METADATA.ome.xml
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I see from
omero-mkngff/src/omero_mkngff/__init__.py
Line 108 in 4c1e32b
We'll need to pick another file to update the pixels table with.
@josh - I can have a go at fixing this, but given my lack of sql
skills, I would move the logic for finding a path/name
from the setup.sql
mkngff_fileset()
function into the main def sql()
function, to add an extra:
self.ctx.out(f"UPDATE pixels SET name = '{name}', path = '{path}' where image in (select id from Image where fileset ={args.fileset_id});
Logic would be: choose METADATA.ome.xml
if it's found, otherwise use top-level .zattrs
.
Let me know if you'd prefer to update mkngff_fileset()
yourself and keep the logic there? - I can hold off on this (and run sql manually for now as at IDR/idr-metadata#650 (comment) for testing)?
That doesn't sound too bad. I wasn't a huge fan of the if
block in the SQL to begin with.