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You are here: Home Community Minutes Conference Calls 2017 2017-08-15-tuesday-team-meeting


Dundee: Will, Simon, Jason, June, Balaji, Mark, Dominik, Roger, Helen, Riad, (Jean-Marie, Seb - 14:14) Remote: Kenny, Josh, Liza, Melissa, Eleanor, Wilma, David, Chris, Emil, Andreas

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Files/Formats/OME Files

        • BioFormats release. 5.6.0
        • Few PRs open later today to update downstream usage
      2. Formats meeting this week to discuss next steps

      3. Metadata

        • IDR 4.3 plan. Data ready for releasing but a few bugs still to fix
        • Could delay release or just release data but not code?
      4. Balaji: Notebooks - running on 30 different complexes, looking at genes wrt GO

      5. PR for IDR py.

      6. OMERO 5.4.0

        • Mark: Petr discovered security vulnerability for light admins
          • does not affect OMERO 5.3
          • light admins could work with official scripts without WriteScriptRepo
          • now fixed bug and adjusted the test that ought to have checked this
        • Mark: performance of deletion with heavily linked annotations
          • severely affects IDR data management workflows
          • speculative fixes did not help
          • culprit: previous testing suggested Hibernate's caching
            • would like to confirm but difficult to profile server under sufficiently heavy load
            • our Hibernate is several years old
              • there is reason to expect better from newer Hibernate
          • culprit: database trigger for reindexing
            • slowest part is a fix for an even worse performance issue
            • move to Elasticsearch may make trigger unnecessary
          • for 5.4.0 planning a workaround
            • 5.3 automatically deleting orphaned comments, etc. makes sense as a default
            • find a way to extend server API to block orphan checks enough to return to 5.2 performance
              • should be quite feasible
              • IDR scripts could then activate workaround as needed
        • Mark: poorer server performance under concurrent write operations
          • reproducible via concurrent imports or moves
            • have not tested concurrent read operations
          • suspicious of _current_admin_privileges database table
            • possibly overengineered when fixing earlier issues with flakiness
            • Josh is reviewing the approach
            • can try again to aim for transaction-local table entries
            • however, Petr found postgres processes not consuming much CPU
          • plan to profile* to see if Petr missed any smoking guns
          • not yet confidently identified any promising solution
        • JRS: longer-term interest to upgrade Hibernate or get 5.4 out?
        • Hibernate upgrade likely to take a while
          • Dependent on replacing search
        • Mark: re: 5.4 blockers: Certain concurrent actions can be slower in 5.4
        • Might be able to reduce over-engineering in some places
        • Option to add profiling to look for smoking gun
        • Other
          • Will: Adding tests on existing functionality
          • J-m: rolling out testing devspaces
          • TBC
      7. Outreach

        • Cambridge December discussion - Gabriella to start gdoc for advertising course
        • 2 day course - each day independent. Day 2 advanced
  3. Other releases/upgrades:

    1. Figure & iViewer

      • ROI functionality in iViewer. Shape dimensions/stats.
      • Some code might need to be moved down to server (new microservice in future)?
      • FPBioimage discussion with Michael - e.g. ROI support (cropping)
    2. new website

      • Seb: No active changes just now
      • Secvuln pages migration from old site to new
      • Other content & resourses. Movies, Training etc.
      • Kenny: site support url redirects. No www.legacy...
    3. Sysadmin (current board and recent PRs)

      • Trout re-imaging: Issues with disks. Carp (VM) to be replacement
  4. Glencoe Update: Chris

    • Masks support in OMERO.web and pathviewer
    • Few existing issues. Colour mapping & display
    • Also rendering and handling pngs
    • Masks are ‘full image’ in use cases (very large X and Y sizes)
    • Tiling of masks needed
    • Rendering engine fixes to go into 5.4.0 possibly?
  5. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - Upgrade latest git etc (secvuln fix)

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