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Task #4167 (new)

Opened 9 years ago

Last modified 4 years ago

Writers do not support overwriting metadata

Reported by: mlinkert Owned by:
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: OMERO-5.2.0
Keywords: export Cc: simon.blanchoud@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See attached test case. In summary, writing some subset of planes using one MetadataRetrieve? then closing the writer, re-initializing with a different MetadataRetrieve?, and writing the remaining planes does not have the desired effect.

Attachments (1)

OverwriteTest.java (898 bytes) - added by mlinkert 4 years ago.

Download all attachments as: .zip

Change History (5)

comment:1 Changed 9 years ago by jmoore

imported from bio-formats:#591

comment:2 Changed 8 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.4 to Unscheduled

comment:3 Changed 7 years ago by mlinkert

  • Keywords export added

Changed 4 years ago by mlinkert

comment:4 Changed 4 years ago by mlinkert

  • Owner mlinkert deleted
  • Version set to OMERO-5.2.0

Re-attached original test code, which is old enough that it likely needs to be updated before being usable.

I think it's still up for debate whether this can reliably be resolved at the writer level; what we've been telling people to do for OME-XML/OME-TIFF is effectively this:

https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/utils/FileWriteSPW.java#L397

I'd be OK with this being closed if any combination of the following are done:

1) the post-processing solution in FileWriteSPW is more obviously documented as the correct way to do this
2) a limited set of post-setId metadata changes are allowed (e.g. SizeZ, SizeC, SizeT), possibly for OME-TIFF only
3) an example is written up detailing how we expect writing OME-TIFF at acquisition time to be done

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