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You are here: Home Community Minutes Conference Calls 2017 2017-04-25 Tuesday Team Meeting

2017-04-25 Tuesday Team Meeting

Dundee: Will, Helen, Mark, Petr, Dominik, Jean-Marie, Simon, June, Simone, Balaji, Jason, Kenny, Roger Remote: Josh, Seb, Melissa, David, Andreas, Liza,

Agenda - 2:00pm Start

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Files/Formats/OME Files (Sebastien)
        • First review of tiling benchmark results from David on Wednesday
        • Not public yet, but available internally gdoc
        • BF started new minor release cycle - Large format changes, no API changes
        • Olympus OIR format, from Glencoe. Public sample data.
        • ndpis format - target to release next week & include in OMERO 5.3.2
      2. Metadata (Josh)
        1. Paper edits & new URL
          • Resubmit soon.
          • Drop -demo from url.
        2. IDR 0.3.6/7 ‘production’ not demo
          • Update urls everywhere
        3. IDR 0.4.0
          • Ola’s work. PRs rebased, everything green
          • New server e.g. “idr next”
          • Enable figure, iViewer etc?
      3. OMERO 5.3.2
        1. 5.3.1 out last week
        2. Only "key" cards for the 5.3.2 release - moving trello cards to new board
        3. Focus on User meeting see point below
      4. OMERO 5.4.0-m1 (Petr/Mark)
        • Mark: OmeroWeb integration test failures fixed, thanks to Will
        • Mark: may have finally fixed rare group-related flakiness in import
        • Mark: working on improving performance
          • finally got profiling working
            • with the help of, omero.jvmcfg.append -Xverify:none
            • identified bottlenecks
          • proceeding with some adjustments to server code to check their effect
        • Petr: live demo
      5. Outreach
        1. Janelia report (Josh)
          • Longer notes on card on outreach board
          • first days “very biological”
          • Lots of new imaging modalities
          • New pieces of metadata
          • ‘expansion microscopy’ - original pixel size -> x4
          • nDim - multiple lasers in various dimensions etc
          • Correlative microscopy common theme
          • Often using matlab notebook to bring everything together
          • Day 3, more computational
          • Brain imaging etc
          • Janelia DVID - ndim service for looking up blocks (binary data). Can we make use of this?
          • czi - nice presentation
          • hdf5 formats and other new formats.
          • ITR ‘image tool resource’ project.
          • e.g.
          • Available data & platform for algorithms to solve various challenges
    2. Other releases/upgrades:

      1. Figure
        • Released 3.0.0
        • Need to review 3.0.1 board priorities
        • Release last week
      2. iviewer
        1. Reviewing UI - Will: prototyping in Photoshop
        2. Consistency between apps figure, webclient, iViewer
      3. new website
        • Working on Content for few remaining pages
        • Explore OME in Action page to link to Demos etc.
        • Developers getting started page needs content
      4. Sysadmin (current board and recent PRs)
        • 5.3.1 upgrade of nightshade
        • GPFS -linked machine with VM for ansible
        • Ports issue - limited ports for connecting to external machines/servers
        • JM: mtools release for OMERO 5.3.x
    3. Glencoe Update (Chris)

      • webinar prep (tomorrow)
      • oir etc.
      • Emil & Melissa here for Users meeting
    4. User meeting update

      1. Analysis - Josh
        • Analysis POTN board
        • 2 or 3 workshops might include analysis work
        • Biological tasks - few examples, more suggestions welcome
        • Jason: analysis tools make for nice demos for other events / workshops & useful for testing etc.
        • Josh: getting metadata into IDR so that it’s useful/accessible to other tools. Where to store metadata in what format. Jason: and generating it as automatically as possible.
        • Jason: need to put names to workshops. Probably after standup later this week:
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    1. Josh: upcoming "proposals" (queues & tiles)
      • Help users/satellites to solve hard problems
      • OSARs scheduled for after users’ meeting, in June.
  4. Roles Demo (Petr):

    • New role demo, “administrators with restricted privileges”, or “Light Admins”
    • Rationale:
    • super-users, acting for other users, e.g. “Analyst”, “Importer”,
    • Not group-specific, but need to access data from many groups
    • BUT, not ‘Full Admins’ of the server. Limited privileges.
    • Balance to provide enough power, but not too much
    • Webadmin UI:
    • create/edit user form has link to “administrator privileges” docs
    • Docs has table of permissions required for various use-cases
    • e.g. “Manager” / facility manager includes Sudo, Chgrp, Chown, Create/Edit groups/users.
    • In general aim to prevent accidental damage/delete etc
    • Demo of workflow of “Manager” role
    • Light-Admin cannot edit their own Privileges
    • Create Groups & Users
    • When Light-Admin creates users, should only be able to create regular users (not admins OR light-admins).
    • Josh: client UI and server should allow same! (don’t make client more restrictive)
    • bin/omero --sudo manager -u newbie -g othergroup login # Manager login as newbie
    • Can then create Dataset as newbie, import as newbie etc.
    • In webclient UI (not sudo) use chgrp permission to Move to new group.
    • Bug: try to add comment in read-only group not disabled in webclient
    • CLI chown to new user.
    • Bug: thumbnail creation for non-owner in new group in webclient UI?
    • Bug: CLI insists that user must be in target group to chgrp (webclient doesn’t)
    • Insight ‘import as’ doesn’t show all groups
    • Jason: important to remember (remind users) who you are logged in as.
    • Josh: e.g. sudo in webclient - show prominent indicator. Jason ‘red and bold!’
    • Jason: nice demo, thanks!
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