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You are here: Home Community Minutes Conference Calls 2014 2014-09-09 Tuesday Team Meeting

2014-09-09 Tuesday Team Meeting

Dundee: Kenny, Gus, Will, Petr, Emil, Ola, Blazej, Helen, Dominik, Balaji, Andrew, Graeme, June, Remote: Josh M, Ian, Melissa, Colin, Kelli, Seb, Wilma, Yuriy, Josh B, Curtis, Mark, Douglas

Dundee: Kenny, Gus, Will, Petr, Emil, Ola, Blazej, Helen, Dominik, Balaji, Andrew, Graeme, June, Jean-Marie, Simone, Roger Remote: Josh M, Ian, Melissa, Colin, Kelli, Seb, Wilma, Yuriy, Josh B, Curtis, Mark, Douglas

Notes

  1. Project Status (15 minutes max)

    1. Mainline (5 minutes)

      • Still working from proposed scheduled (nitpick)
      • Change based on stability of develop schema
      • Upcoming releases (5.0.5 & 5.1.0-m1)
      • Backport requests on the “Priorities List” board
      • Brief discussion about update sites
        • Jars are downloaded from d.o.org and then served from ij servers
        • Curtis: like the develop plan; users want “stable” or “latest”
    2. Glencoe Update (5 minutes) - 14:44 UK

      • JB still working on ORM layer and updating jars (see PR 3000)
        • travis builds are green; but server doesn’t start.
        • indexer & pixeldata are complaining that they don’t have a session.
        • more eyes welcome.
      • Stick & Emil working on cellprofiler
    3. Consortium Update (5 minutes) - 14:47

      • Ian: thanks for the release? re: GUI - hope not reproducing the wheel?
      • Seb S.: nothing in particular
      • Mark/Curtis: update by the end of the week; work on scripting parameters
      • Douglas: jquery update! Eyes welcome. Lots of little things are possibly broken.
        • Will to look later today
    4. Simone - 'Integrating Hadoop into OMERO, Update 2014-09-09' (20-25 minutes plus 15 mins questions max)

      • IO backend work to have HDFS backend for path.py
        • Bigger picture: FS abstraction layer for OMERO
      • Scalable backend for numerical data
        • Currently looking at SciDB & Apache Spark (basis for ADAM)
      • Feature calculation with WND-CHRM
        • distributed version with pydoop script
        • in new repository pydoop-features
        • Simon added number crunching part in his fork
        • working on bundle which installs everything on the fly on the cluster
      • HDFS In/Out
        • Simon has exported numpy arrays via an OMERO script
        • array extraction directly from HDFS would require direct Bio-Formats access
        • storing back in to OMERO is a further problem
        • path.py update PR under review
        • fixed Pydoop unicode issues
        • work is scattered over a number of repos/branches
        • CRS4 developing (incl. a new dev) a mostly pure Python rewriting of Pydoop's backend (performance-critical (de)serialization section will probably stay in C/C++)
        • want everything merged back into develop as soon as possible
        • could move to pathlib; only in Python3 mainline though there is a backport
          • there is an FS abstraction layer in Hadoop itself.
      • Josh: primarily concerned with the synchronization between Python & Java
        • Simone: can some version start expecting URIs? fork for HPC?
    5. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

      • J-m: workshops (c++ last Wednesday)
        • idea to move to Tuesdays; optional in case not of interest
        • keep project review beforehand short (~20 minutes)
        • upcoming: code gen (Josh while in Dundee)
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