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You are here: Home Community Minutes Conference Calls 2015 2015-01-13 Tuesday Team Meeting

2015-01-13 Tuesday Team Meeting

Dundee: Emil, Chris, Kenny, Gus, Mark, Will, Dominik, June, Andrew, Petr, Helen, Simon, Ola, Roger, Balaji Remote: Jean-Marie, Josh M, Yuriy, Sebastien B, Colin, Ian, Kelli, Stick, Melissa, Mark H, Wilma, Curtis, Josh B

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. Project Timelines (2-3 minutes each)

    1. Core (incl. CI & QA) (Josh) - 14:31 UK

      • Versions: see
        • RFC sent out to mailing lists
      • Maps/Scripts/others: all UI changes should be in by end of January
        • Jean-Marie: Will has PR open to show ongoing work on MapAnnotation
      • Rendering: work beginning next week
        • scope reduced for 5.1, XML model changes pushed to 5.2
          • Jean-Marie: haven’t dropped work wholly, will send out proposal
          • Josh: one step is likely to be XSD representing what is currently in database for rendering settings
      • libbioformats: currently finishing up the last item from m3 (moved to m4), the OMEXMLServiceImpl conversion, after which we should have all the code for metadatastore to work and to move on to the OME-TIFF implementation.
      • Last minute:
        • QA2
          • working out migration from one system to the other
        • Java
          • Java 6, 7, 8 support issues; need to improve Java 8 support for 5.1
            • Chris: first bits of app bundler stuff ready, probably some Insight work required
        • jstree
          • whole body of work probably not ready soon enough for 5.1
            • Will: problem is Hibernate projection bug?
              • Josh: yes, but that’s not the only significant issue
              • Will: Douglas had a workaround?
              • Jean-Marie: workaround would be very painful as would require full code review again
              • Chris: still many UI parity issues when compared with 5.0
        • timezone
          • for 5.1 at least warn systems administrators of issues
      • push m4 back a month, so above points ready for freeze by mid-February?
        • requires backports for a 5.0.7 for end of January
        • Chris: will open 5.0 PR for Java 7 launcher
          • Roger: would be valuable for 5.0.7
    2. Glencoe Update (Chris) - 14:48 UK

      • team meeting in coming weeks regarding digital pathology viewer
        • more HTML5 and ROI work, involves both server and client
        • using different library for tile-drawing
    3. Virtual Microscope/teaching (Ola) - 14:52 UK

      • PG encoding being updated. See
        • Kenny: working on process of changing collation, etc. from LATIN1 to UTF8; then will arrange downtime
          • Josh: could be good to describe process in systems administrator documentation for other users
      • ROI annotations mockup. See
        • Jean-Marie: mockup is fairly simple, not a great change from what we have; does not preclude larger changes in the long term
      • Josh: plans for upgrading virtual microscope to 5.1?
        • Ola: once Kenny has changed database character encoding, hoping to upgrade to m3 soon before classes start
        • Josh: will need to test on staging
    4. FLIMfit/OPT (Ian) - 14:56 UK

      • Close to finishing integration of Java widget into FLIMfit
      • Primary issue is distribution. Can it be built/distributed as part of OMERO? If that’s premature, then I can stick the src and the .jar into the FLIMfit repo but I could do with some assistance here. Could somebody with Maven/Ant chops find the time to help me to add whatever might be needed/expected to allow people to build the .jar from the source. I’m using Netbeans for this step so this is all unfamiliar territory.
      • Could be a useful example for others creating OMERO clients.
      • Jean-Marie: will take a look over coming days
    5. Bio-Formats large file sets (Sebastien B) - 15:00 UK

      • Primary issue is Windows speed. Will require resources for getting automated builds in place (needs mounting of squig, etc)
      • Developer docs ready for 2nd round of review - if Ian & Douglas could look at them over the next week? (Trello card here)
      • No issues raised yet about memoizer
    6. Other consortium timelines (5 minutes) - 15:02 UK

      • Josh: release new OMERO.figure with 5.1?
        • Will: enough work done by then to justify a release
      • Josh: anyone who needs CI, testing, etc. help for their project, let us know deadlines well in advance, as also plenty to get done for planned OMERO releases
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:05 UK

    • FYI: CI rehearsal post meeting
    • Ian: would much like to be able to download plate data
      • Chris: probably not in 5.0.7 nor 5.1.0
      • Will: not too far away, except for the issue of large data
      • Chris: serious large data download issue if making plate download publicly available for all plates
        • all possible to solve, but would take enough development time to not be near-term
      • Ian: these plates are simply single OME-TIFF files
        • Will: makes it even easier
        • Mark: will provide suitable test file

Done 15:11 UK

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