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20240118-minutes.md

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Imaging Working Group Minutes

Thursday, 2024/01/18

10:00 am ET

Attendees:

Terrell Russell, Kory Draughn, Laura Capps, Mike Conway (NIEHS), Josh Moore (GerBI / OME), Guillaume Gay (France Bioimaging), Pascal de Boer (Groningen), Rodrigo Rosas (Maastricht University), Alice Stuart-Lee (SURF), Judith Lacoste (MIA Cellavie)

Minutes

  • Serialization of OMERO format to iRODS via PRC
    • No NFSRODS
    • AA) 'Save' is working, two commits in PR
      • Python script, uploaded to OMERO, executed with Image payload
      • #30
      • Saves a new data object into iRODS, currently always named 'transfer.tar'
      • DEMO
      • Have to decide where in the iRODS namespace to drop these data objects - just pass a 'full path'? But that requires an OMERO user to 'know' where they want it to go in iRODS (iRODS knowledge). Could be derived/generated from the 'open' files in OMERO.
      • Have to determine naming structure for data object (timestamp? Username? User gets to pass a string for the named file? Concatenation of all of these?)
      • Mapping of OMERO user to iRODS users and permissions and passwords
        • No place to store secrets, currently OMERO user info is just hashed passwords in OMERO db or in LDAP
        • When in a browser, can just OAuth/OIDC everywhere else needed
        • COULD just be that OMERO is always just a service account (a single irods user), and attach a payload/instructions for some policy on the iRODS side to open/parse/takeaction
          • Simpler, no additional code on the OMERO side
          • Complex, more code on the iRODS side
      • Scripts not currently interactive with the user - so cannot prompt the human for credentials
      • Want to make sure no overwriting existing data in iRODS
      • No delay/async mechanism in OMERO proper
        • Past users have done async operations 'out of band'
        • Would just do the same here, pushing to subprocess
    • BB) Load - Read snapshot from iRODS into active OMERO object
      • Would create a new instance, could overwrite something in OMERO, TBD
    • CC) List - shows the existing snapshots in the iRODS side
  • Transfer Tool TODO
    • On OMERO side, tar gets created, then gets pushed…
    • Should be possible, to NOT copy… possibly using libarchive(.c)?
    • Plan for long-term support for archives.
  • Do we need to support more than one iRODS Zone?
    • I think this is 'solved' by the user abstraction layer on the OMERO side
    • Will need a secure place in the OMERO server OR a mapping/pointer into an already secure area
  • Next time - research
    • How does Bisque interconnect work? Users? Secrets? Memory footprint? Async?
  • France Bioimaging
  • Next Meeting
    • Feb 2024