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20240215-minutes.md

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Imaging Working Group Minutes

Thursday, 2024/02/15

10:00 am ET

Attendees:

Terrell Russell, Kory Draughn, Josh Moore (GerBI / OME), Joost Willemse (Leiden University), Ander Astudillo (SURF), Alice Stuart-Lee (SURF), Guillaume Gay (France Bioimaging), Marjolijn Mertz (NKI - Netherlands Cancer Institute), Nirav Merchant (CyVerse / UArizona), Rolf Harkes (NKI - Netherlands Cancer Institute)

Minutes

  • Serialization of OMERO to iRODS via PRC
    • AA) Save (As)
      • Josh added target data object location for saving into iRODS namespace
        • No longer just named 'transfer.tar'
        • Leaves naming decision to the human
        • They have to know where they can save a datafile
        • Overwriting will happen today without first checking the target
        • What does error handling look like? Bad path / bad permissions?
          • Josh - any errors will be shown in the OMERO UI
      • Currently hard-coded user/pass combo to talk to iRODS
        • OMERO could hold an annotation for username
        • But nowhere to get passwords at this time
          • OIDC would be favorite if possible
          • Only OMERO-web viable for now
            • Other clients don't know how to do this fancy web stuff (yet)
        • Inital work/success will just be 'service account'
          • Assume iRODS admins will handle the 'archive' side
        • Mapping file of usernames generated by admins
          • iRODS rodsadmin session can proxy as the correct user
        • Current OMERO LDAP integration uses OMERO email/username OR an LDAP query
    • BB) Load
      • Could/Should just be a flag on the same script to read/load?
      • Should it be able to overwrite in OMERO?
        • Would have to be a delete flag? Maybe doesn't make sense.
        • Would always upload/create a new ID in OMERO
  • Looking for guinea pigs
    • If you'd like to archive OMERO information into elsewhere… this script provides a means to do that
    • Nirav - has a use case, NIH data management plans - if people ask for access to your data, this could provide a means to bundle a study to share with another OMERO user or elsewhere. The storage system can be exposed for sharing without exposing the OMERO instance to others.
      • This is a vote for Save and Load
  • Joost - so this would not reuse the same ID in OMERO? … correct
    • What happens if OMERO data is deleted?
      • The archive/saved version is independent / decoupled
  • Alice - Dutch Bioimaging also interested in testing this
  • Guillaume - If you delete the raw-data in OMERO the annotations and thumbnails stay so you could have a way to keep a 'trace' of archived data (out of scope for this group)
  • Consortium
    • Check for overwrite/existence before sending/saving
    • Confirm errors are sent back to OMERO
    • Consider bidirectional save/load in the same script
    • Think about mapping file
      • What happens when no user found…
  • Next Meeting
    • March 2024