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You are here: Home Community Minutes Conference Calls 2016 2016-12-06 Tuesday Team Meeting

2016-12-06 Tuesday Team Meeting

Dundee: Petr, Kenny, Gus, David W, Mark, June, Jean-Marie, Simon, Dominik, Will, Balaji, Simone, Ola Remote: Josh M, Harald, Andreas, David G, Eleanor, David, Emil, Roger

Agenda - 2:15pm Start

  1. Accepting minutes from last meeting

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

    1. Spaces - 14:14 UK

      1. Files/Formats/OME Files (Sebastien)

        • Bio-Formats 5.3.0
          • Options and tiling API integrated: ongoing work on enabling tiled writing, Zeiss CZI options and option propagation to subreaders.
          • Set of code-generation and OME-XML bug fixes: enabling of ROI functionality (Mask.BinData, Transform) from Model to OMERO
          • Feature freeze tomorrow. Working on testing, usability, documentation and bug fixes.
        • OME Files 0.3.0
          • Initial proposal for handling extended metadata in the model
          • Ongoing investigation of the FileAnnotation to generically describe and represent external files (csv, txt..)
      2. Metadata (Josh)

        • Several pressing issues for 0.3.1 (pre-holidays)
        • Annotation correctness
        • Scalability (idr0009)
        • awstats/ELK
        • 0.3.2: rendering
        • visualization of logs, capture what users are wanting to see
        • Multimot next weekt, visitors to Dundee
        • considering decoupling metadata & ROI populate scripts from repository to share among metadata, mainline, etc.
      3. OMERO 5.3.0 (Jean-Marie)

        • Preparation for 5.2.7 release ongoing mainly sysadmin release
          • will get 5.2 CI jobs, release board, etc. all up
        • 5.3.0:
        • won’t drop support for Java 1.7
        • work on migration from eel to seabass: Part of CentOS 6 support drop
        • clients: ready for “screenshots”: histogram and SPW grid view
        • web apps now mostly cleaned up. Some work to be done on webtest
        • ongoing on testlib: python testing library.
        • Web API:
          • we will have probably a quick chat post standup every second day
        • Ongoing work on light administrator roles
      4. Outreach

        • Balaji working on “import” video (CLI)
          • finding and reporting some bugs along the way
    2. Other releases/upgrades - 14:25 UK

      1. Figure (Will)
        • code tidyup
        • Balaji's PR for maintaining aspect ratio
      2. iviewer:
        • New repo (see presentation)
        • Working on jobs now so we can include in daily review
      3. Learning
      4. Sysadmin (Kenny)
        • looking at how to move services into Dundee-hosted OpenStack
          • maybe even nightshade early next year depending on how it all goes
      5. Website redevelopment/redesign (Liza)
        • Helen: plan is now to finish content ready for Liza to apply design elements when she's back from maternity leave in May. I'll probably set up a new Trello board and we'll need to sort out merging Liza's work so far into the main repo and setting up a staging build so we can move to a proper PR workflow and more people contributing and reviewing in the new year.
        • Josh: Would be good to have overall outline, pages, text, etc. together for when Liza returns from maternity leave
      6. Smuggler (Montpellier)
    3. Glencoe Update (Emil) - 14:29 UK

      • elasticsearch work
      • preparing for performance work
      • read-only effort
      • JPEG-XR API
      • Jean-Marie: may need to discuss plate naming PR from Melissa
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 14:30 UK

    • June: busy with end-of-year finances
    • Josh: last call to protect instances on beluga from being wiped
  4. Status update on OMERO.iviewer (formerly viewerng) by Harald - 14:31 UK

    • Will: don't yet show hierarchy of shapes in ROI?
      • Harald: indeed, not yet
    • Will: ran into some issues with saving and deleting with propagation across planes
      • Jean-Marie: few issues have been noticed, add to the Trello card
      • Harald: latest version should already work fairly well
    • Jean-Marie: need measurement tool stuff for pixel intensities in ROIs, etc.
      • Dominik added useful code for this to the Java gateway
      • Jean-Marie: given measurement and folders can supersede Insight's measurement tool
    • Jean-Marie: when installing could select preferred viewer
      • Will: open with
      • Josh: what about testing? two different webservers? open with?
        • Jean-Marie: looking into getting into merge build
      • Josh: not have img_detail in URL
    • Ola: direct link to zoom level, etc.?
      • Harald: not compatible at present, partly due to openlayers' different API
    • Will: URL refers to dataset or image?
      • Harald: currently image-centric URLs, then looks up dataset
      • Will: issue with images in multiple datasets
      • Jean-Marie: would be nice to be able to open a dataset
      • Balaji: SPW support?
        • Harald: nothing yet, just see the image, nothing extra from plate
    • Josh: how to proceed on questions like styling/CSS ?
      • Jean-Marie: sorting out CI workflow first then can add to standup
        • maybe own devspace or WEB-DEV-merge-deploy
    • Petr: how are affine transforms handled?
      • Harald: can display rotated ellipse but requires more work
      • Jean-Marie: meeting with Michael P, probably Friday, to synchronize/unify
    • Harald: also yet to retrieve via omero-marshal
    • Balaji: what of the freehand ROI, how is it stored in OMERO?
      • Harald: polyline or similar, many coordinates; can infer it's freehand from point density

Done 15:08 UK

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