omero admin cleanse: handle missing directories in the ManagedRepository#492
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sbesson merged 1 commit intoome:masterfrom Mar 25, 2026
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This commit tries to improve the handling a ManagedRepository directory registered in the database but missing from disk. Currently, `omero admin cleanse` fails with a `SecurityViolation` server error as per the contract of `repo.listFiles()`. This change catches the server error, logs the message in the command output with an `ERROR` prefix and returns `False` to indicate no empty directory was found. This mechanism should allow the command to continue scanning the ManagedRepository, report other errors or empty directories and provide a more complete audit allowing the administrator to review and take the appropriate action.
kkoz
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Feb 17, 2026
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Works as expected. Without the patch, I get
omero.ValidationException: exception ::omero::ValidationException
{
serverStackTrace =
serverExceptionClass =
message = /kevin_2/2026-02/17/ does not exist
}
But with it I get
/OMERO/ManagedRepository
ERROR: /kevin_2/2026-02/17/09-41-29.533/ does not exist
mabruce
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Mar 24, 2026
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Worked for me. The directory check reported an ERROR for the missing directory and then proceeded to check the rest of the ManagedRepository.
omero admin cleanse --dry-run --subdirectory ManagedRepository --verbose /OMERO
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This commit tries to improve the handling a ManagedRepository directory registered in the database but missing from disk. Currently,
omero admin cleansefails with aSecurityViolationserver error as per the contract ofrepo.listFiles().This change catches the server error, logs the message in the command output with an
ERRORprefix and returnsFalseto indicate no empty directory was found. This mechanism should allow the command to continue scanning the ManagedRepository, report other errors or empty directories and provide a more complete audit allowing the administrator to review and take the appropriate action.To reproduce the issue:
omero importto create a new/OMERO/ManagedRepository/<user>_<id>/<YYYY>-<MM>/<DD>/<hh>-<mm>-<ss>-<SSS>directory under the databaseomero delete, this should delete the original file and the import log but keep empty directories/OMERO/ManagedRepository/<user>_<id>/<YYYY>-<MM>/<DD>/<hh>-<mm>-<ss>-<SSS>/OMERO/ManagedRepository/<user>_<id>/<YYYY>-<MM>/<DD>/With OMERO.py 5.22.0,
omero admin cleanse --dry-run /OMEROshould fail with aSecurityViolationmessage similar/<user>_<id>/<YYYY>-<MM>/<DD>/ does not existand abort.With this PR included, the same command should log the error message indicating the folder does not exist but continue processing the binary repository.