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Add a script to edit path of in-place imported images#2

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Tom-TBT wants to merge 2 commits into
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inplace_edit
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Add a script to edit path of in-place imported images#2
Tom-TBT wants to merge 2 commits into
mainfrom
inplace_edit

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@Tom-TBT Tom-TBT commented May 18, 2026

New script to work on the path of in-place imported images.

The script aims to validate the changes as much as possible before editing the path stored in the database and before editing the symlinks.

  • Same checks as the Fileserver_import script (user is allowed to access data on the target fileserver, no backward reference)
  • Ensure that path to replace is found only once (no ambiguity allowed)
  • All new path are targeting files from the same Group from the data access validation (cf Fileserver_import config)
  • New symlink points to a valid file
  • Target file have the same size as the old
  • opt: target file checksum matches the old checksum
  • Updated images are in-place imported
  • User has permission to edit the Fileset object in OMERO

Once that the checks pass, the symlinks are created in three steps:

  • Generation of a temp symlink
  • Deletion of old symlink
  • Renaming of the temp symlink
    If this is successful, then the clientPath of the Fileset_Entry is updated.

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