Importing ome metadata to omero server fails with ".zarr.ome.xml" files
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- Java
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Description
I am currently experiencing an issue when attempting to import the ome xml metadata associated with a zarr file. I do not want to import the images only the metadata that is stored within the ome.xml file.
Reproduce
I am using the omero import command to upload the ome.xml files to my omero server. The first file dummy.zarr.ome.xml fails to be uploaded, but the second file does not fail and is update as expected to the server. Note that the only difference between the files is the name of the file, one ending with .zarr.ome.xml and the other .ome.xml. Both files can be downloaded from here:
dummy.zarr.ome.xml
dummy_v2-zarr.ome.xml
To reproduce the error, I am using the following commands.
FILE="./dummy.zarr.ome.xml"
omero import -d $DATASET_ID -k $SESSION -s $OMEROSERVER $FILE --debug DEBUG
FILE="./dummy_v2-zarr.ome.xml"
omero import -d $DATASET_ID -k $SESSION -s $OMEROSERVER $FILE --debug DEBUG
I have also attached the complete output that I get in the terminal in this output.txt file.
Notes
It does not seem to be only related to the name of the file. I can upload ome xml files that end with .obf.ome.xml, .msr.ome.xml, .tif.ome.xml, etc. without any issues.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the two omero import commands in the issue and compare their debug output with output.txt. Trace how the importer handles dummy.zarr.ome.xml versus the working .ome.xml and other supported suffixes. Done means the zarr-associated OME-XML file imports its metadata without importing image data, while existing suffixes continue to work.
Written by the indexing model from the issue text.
Assessment
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100