Importing ome metadata to omero server fails with ".zarr.ome.xml" files

[antho214]

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.

[will-moore]

Bio-Formats uses the name and extension of files to guess which reader to use.
Since the name contains .zarr, the ZarrReader is chosen:

2026-03-23 14:34:44,944 487        [      main] DEBUG                loci.formats.FormatHandler - ZarrReader initializing /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml

And then it tries to find the file that ends with .zarr but fails:

java.io.IOException: Path '/home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr' is not a valid path or not a directory.

It's possible the logic could be improved, but it's probably easier for you to rename you files. Since you're not importing a Zarr file, you should be OK to remove the .zarr from the name?

You can still give the Image a name in the ome.xml metadata, which should be used to name the new image?

[antho214]

Thank you for the information! Indeed, renaming the file should not be too much of an issue.
Do you suggest that I open an issue in the ZarrReader package so that they are aware of this behaviour? As I said this behaviour only seems to be related to the .zarr.ome.xml.

On a side note, I also attempted to use the -l option when importing the files. In theory, this option would allow to give a list of readers from which to use. Though in my hand all of the following failed with the Could not find xxxxxx

omero import ... -l OMEXML
omero import ... -l OMEXMLReader
omero import ... -l loci.formats.in.OMEXMLReader

[dominikl]

Sorry, the help text of the import command - although correct (-l READER_FILE) - could be clearer. You have to pass a text file to the -l command which contains a list of readers which should be attempted. I.e. in your case:

echo "loci.formats.in.OMEXMLReader" > /tmp/reader.txt
omero import -l /tmp/reader.txt ...

[antho214]

I have attempted to use the -l option. It looks like it is selecting the right reader, but I am getting another error as if the file cannot be created. I have attached the logs below.

output.txt

[will-moore]

Hmmmm, it looks like the correct reader is being used, and the file is uploaded, but then ZarrUtils is again looking for the .zarr directory. Any ideas @dominikl ?

...
2026-03-25 15:02:14,907 485        [      main] INFO                   loci.formats.ImageReader - OMEXMLReader initializing /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml
2026-03-25 15:02:14,907 485        [      main] DEBUG                loci.formats.FormatHandler - OMEXMLReader initializing /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml
2026-03-25 15:02:14,907 485        [      main] DEBUG                loci.formats.FormatHandler - loci.formats.in.OMEXMLReader.initFile(/home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml)
2026-03-25 15:02:14,913 491        [      main] INFO                 loci.formats.FormatHandler - Populating metadata
...
2026-03-25 15:02:21,349 6927       [3-thread-1] INFO   ts.importer.transfers.UploadFileTransfer - Transferring /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml...
2026-03-25 15:02:21,473 7051       [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml
2026-03-25 15:02:21,618 7196       [3-thread-1] DEBUG  ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES uploaded: 0 of: 1505 bytes (ETA: 0' 0")
2026-03-25 15:02:21,694 7272       [3-thread-1] DEBUG  ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES uploaded: 1505 of: 1505 bytes (ETA: 0' 0")
2026-03-25 15:02:21,891 7469       [3-thread-1] DEBUG  formats.importer.transfers.TransferState - anbil106_3/2026-03/25/19-02-20.610//dummy.zarr.ome.xml id=1022
2026-03-25 15:02:21,891 7469       [3-thread-1] DEBUG  formats.importer.transfers.TransferState - checksums: client=84e76448d6664d29f4a800752053ec82b147ac15,server=84e76448d6664d29f4a800752053ec82b147ac15
2026-03-25 15:02:21,892 7470       [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml
2026-03-25 15:02:22,241 7819       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2026-03-25 15:02:22,825 8403       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 1021
2026-03-25 15:02:22,902 8480       [l.Client-1] DEBUG  ormats.importer.cli.LoggingImportMonitor - INTERNAL_EXCEPTION: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy.zarr.ome.xml
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {stacktrace=java.io.IOException: Path '/OMERO/ManagedRepository/anbil106_3/2026-03/25/19-02-20.610/dummy.zarr' is not a valid path or not a directory.
	at com.bc.zarr.ZarrUtils.ensureDirectory(ZarrUtils.java:156)
	at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:94)
	at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:87)
	at loci.formats.services.JZarrServiceImpl.getGroupAttr(JZarrServiceImpl.java:104)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:166)

[dominikl]

Could you try to rename dummy.zarr.ome.xml to dummy.ome.xml? I wonder if the ZarrReader - now on the server side - still tries to pick that up because the file has ".zarr" in the name.

[antho214]

When the file is renamed to dummy.ome.xml I do not need to specify the the -l as mentioned in the original post. With the -l option and the filename renamed to dummy.ome.xml there is no error.
Again this is not an issue per se to rename the files. However, the same procedure using similar filenames convention (e.g. dummy.msr.ome.xml, dummy.stk.ome.xml, dummy.czi.ome.xml) works without any issues. Hence, I think this is more related to consistency across the different readers.
Thank you for the help.

...
2026-03-26 07:24:02,768 481        [      main] DEBUG     ome.formats.importer.cli.ErrorHandler - SCANNING: Depth:0 Num:    1 Tot:  n/a File: _v2-zarr.ome.xml
2026-03-26 07:24:02,771 484        [      main] DEBUG                     loci.formats.Memoizer - skipping memo: no directory given
2026-03-26 07:24:02,773 486        [      main] DEBUG         loci.common.NIOByteBufferProvider - Using mapped byte buffer? false
2026-03-26 07:24:02,774 487        [      main] INFO                   loci.formats.ImageReader - OMEXMLReader initializing /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
2026-03-26 07:24:02,774 487        [      main] DEBUG                loci.formats.FormatHandler - OMEXMLReader initializing /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
2026-03-26 07:24:02,774 487        [      main] DEBUG                loci.formats.FormatHandler - loci.formats.in.OMEXMLReader.initFile(/home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml)
2026-03-26 07:24:02,780 493        [      main] INFO                 loci.formats.FormatHandler - Populating metadata
2026-03-26 07:24:02,781 494        [      main] DEBUG       loci.common.services.ServiceFactory - Loaded properties from: services.properties
2026-03-26 07:24:02,782 495        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface ome.codecs.services.JAIIIOService and implementation class ome.codecs.services.JAIIIOServiceImpl
2026-03-26 07:24:02,782 495        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JPEGXRService and implementation class loci.formats.services.JPEGXRServiceImpl
2026-03-26 07:24:02,783 496        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MDBService and implementation class loci.formats.services.MDBServiceImpl
2026-03-26 07:24:02,783 496        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MetakitService and implementation class loci.formats.services.MetakitServiceImpl
2026-03-26 07:24:02,783 496        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.EXIFService and implementation class loci.formats.services.EXIFServiceImpl
2026-03-26 07:24:02,784 497        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JHDFService and implementation class loci.formats.services.JHDFServiceImpl
2026-03-26 07:24:02,784 497        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.NetCDFService and implementation class loci.formats.services.NetCDFServiceImpl
2026-03-26 07:24:02,785 498        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JAIIIOService and implementation class loci.formats.services.JAIIIOServiceImpl
2026-03-26 07:24:02,785 498        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.OMEXMLService and implementation class loci.formats.services.OMEXMLServiceImpl
2026-03-26 07:24:02,786 499        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.POIService and implementation class loci.formats.services.POIServiceImpl
2026-03-26 07:24:02,786 499        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.common.services.S3ClientService and implementation class loci.common.services.S3ClientServiceImpl
2026-03-26 07:24:02,786 499        [      main] DEBUG       loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JPEGTurboService and implementation class loci.formats.services.JPEGTurboServiceImpl
2026-03-26 07:24:02,850 563        [      main] DEBUG                     loci.formats.Memoizer - start[1774524242769] time[80] tag[loci.formats.Memoizer.setId]
2026-03-26 07:24:02,856 569        [      main] DEBUG     ome.formats.importer.cli.ErrorHandler - SCANNING: Depth:0 Num:    1 Tot:    1 File: _v2-zarr.ome.xml
2026-03-26 07:24:02,857 570        [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 88ms. (89ms total) [0 unknowns]
2026-03-26 07:24:02,882 595        [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to omero-server.predis.ca:4064
2026-03-26 07:24:03,908 1621       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2026-03-26 07:24:06,277 3990       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.
2026-03-26 07:24:06,494 4207       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.6.17
2026-03-26 07:24:06,494 4207       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.8.4
2026-03-26 07:24:06,495 4208       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.27
2026-03-26 07:24:06,495 4208       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2026-03-26 07:24:06,495 4208       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2026-03-26 07:24:06,495 4208       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 5.4.0-216-generic
2026-03-26 07:24:08,922 6635       [      main] DEBUG                   ome.system.UpgradeCheck - Attempting to connect to http://upgrade.openmicroscopy.org.uk?version=5.8.4;os.name=Linux;os.arch=amd64;os.version=5.4.0-216-generic;java.runtime.version=11.0.27%2B6-post-Ubuntu-0ubuntu120.04;java.vm.vendor=Ubuntu
2026-03-26 07:24:10,816 8529       [      main] INFO                    ome.system.UpgradeCheck - no update needed
2026-03-26 07:24:10,821 8534       [      main] DEBUG  e.formats.importer.targets.TargetBuilder - Dataset
2026-03-26 07:24:10,972 8685       [      main] INFO          ome.formats.importer.ImportConfig - Using import target: Dataset:5
2026-03-26 07:24:11,282 8995       [2-thread-1] INFO         ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:5
2026-03-26 07:24:11,282 8995       [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary - Main file: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
2026-03-26 07:24:11,294 9007       [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary - Used files before:
2026-03-26 07:24:11,294 9007       [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary - /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
2026-03-26 07:24:11,296 9009       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2026-03-26 07:24:11,317 9030       [2-thread-1] DEBUG   ome.services.blitz.util.CurrentPlatform - recognized current operating system as being Linux
2026-03-26 07:24:12,267 9980       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2026-03-26 07:24:12,427 10140      [3-thread-1] INFO   ts.importer.transfers.UploadFileTransfer - Transferring /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml...
2026-03-26 07:24:12,563 10276      [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
2026-03-26 07:24:12,706 10419      [3-thread-1] DEBUG  ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES uploaded: 0 of: 1505 bytes (ETA: 0' 0")
2026-03-26 07:24:12,784 10497      [3-thread-1] DEBUG  ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES uploaded: 1505 of: 1505 bytes (ETA: 0' 0")
2026-03-26 07:24:13,081 10794      [3-thread-1] DEBUG  formats.importer.transfers.TransferState - anbil106_3/2026-03/26/11-24-11.563//dummy_v2-zarr.ome.xml id=1060
2026-03-26 07:24:13,082 10795      [3-thread-1] DEBUG  formats.importer.transfers.TransferState - checksums: client=84e76448d6664d29f4a800752053ec82b147ac15,server=84e76448d6664d29f4a800752053ec82b147ac15
2026-03-26 07:24:13,082 10795      [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
2026-03-26 07:24:13,404 11117      [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2026-03-26 07:24:14,022 11735      [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 1059
2026-03-26 07:24:14,032 11745      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 1059
2026-03-26 07:24:17,261 14974      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 1059
2026-03-26 07:24:17,940 15653      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 1059
2026-03-26 07:24:17,995 15708      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 1059
2026-03-26 07:24:18,041 15754      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 1059
2026-03-26 07:24:18,251 15964      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /home/anthony/Documents/Neurophotonics-FM-Database/data/omes/dummy_v2-zarr.ome.xml
Image:1024
Other imported objects:
Fileset:130
2026-03-26 07:24:18,254 15967      [l.Client-1] DEBUG     ome.formats.importer.cli.ErrorHandler - Number of errors: 0

==> Summary
1 file uploaded, 1 fileset created, 1 image imported, 0 errors in 0:00:07.507
2026-03-26 07:24:18,329 16042      [      main] DEBUG      ome.formats.OMEROMetadataStoreClient - Logout called, shutting keep alive down.
2026-03-26 07:24:18,330 16043      [      main] DEBUG        ome.formats.importer.ImportLibrary - Initializing log out
2026-03-26 07:24:18,332 16045      [      main] DEBUG        ome.formats.importer.ImportLibrary - Shutting down callback ome.formats.importer.ImportLibrary$ImportCallback@6d5c2745
2026-03-26 07:24:18,332 16045      [      main] DEBUG        ome.formats.importer.ImportLibrary - Shutting down fileset thread pool.
2026-03-26 07:24:18,332 16045      [      main] DEBUG        ome.formats.importer.ImportLibrary - Shutting down upload thread pool.
2026-03-26 07:24:18,332 16045      [      main] DEBUG      ome.formats.OMEROMetadataStoreClient - keepalive shut down.
2026-03-26 07:24:18,862 16575      [      main] DEBUG      ome.formats.OMEROMetadataStoreClient - closing client session.
2026-03-26 07:24:19,067 16780      [      main] DEBUG      ome.formats.OMEROMetadataStoreClient - client closed.

[will-moore]

Unfortunately the goal of "consistency across different readers" is not really possible because the data is structured in different ways for different formats.
For OME-Zarr images, it's quite common to have images named image.zarr/0 and image.zarr/1 etc. (multiple images coming from the same original file, with the OME.xml file with combined metadata at image.zarr/OME/METADATA.ome.xml). To find that file, the ZarrReader looks for *.zarr then looks within that "directory" for the ome.xml.

I don't know why the reader specified on import is not also respected when the uploaded file is read on the server. I'm not an expert on Bio-Formats or OMERO.server but that feels like a much deeper issue.