2019-01-29

Dundee: Petr, Mark, Simon, Dom, Jason, Riad, JM, June,

Remote: Seb, Josh, Andreas, Frances, Chris, David, Melissa

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In

  • Jason: TB-scale Data Import

    • Large imports block OMERO from reliably doing anything else,

      e.g. importing an IDR HPA dataset (several TB, 10⁵-10⁶ images) monopolises OMERO for 1-2 weeks.

    • Several other examples from users wanting to make bulk

      queries to OMERO, or wanting to query and modify millions of objects.

    • Chris: Several customers with toxicology HCS: 1536 wells and

      multiple fields.

  • Idr0050: Temporary unicode problems (OMERO.tables/CSV have

    limited unicode support)

    • Dom: replacing unicodes (current workaround)

  • OME-TIFF/Bio-Formats (Seb)

    • OME-TIFF & WSI

      paper

      • Paper edits in ECDP folder. Submission on Friday.

        Comments welcome!

      • [Need ORCiDs!!]

      • Promoting digital pathology work including pyramid work

      • Submitting to [European Congress on Digital Pathology

        2019</u>](https://www.ecdp2019.org/) Mtg

    • BF 6 Roadmap

      • Targeting rc1 with API freeze by end of the week.

      • Blockers: ImageJ/Fiji, S3, OME-TIFF (pyramidal) samples,

        new format doc

      • Pushing not outstanding tasks to Bio-Formats 6.x

        releases

      • Aiming to release BF 6.0.0 mid-February

• Data-Out

  • 5.4.11 (Seb)

    • Insight was fixed in 5.4.10, command line importer is still

      broken with latest Java release. Fix also added a new client dependency (guava) which wasn’t documented.

    • Current command line importer workaround in 5.4.10: disable

      upgrade check/

    • Decision: release a fix in 5.4.11 or wait for 5.5.0?

      • Probably wait for 5.5.0 to save time, PR can be

        backported to the IDR branch.

      • Chris: Glencoe has workaround for client dependency so

        release not critical, but everyone should take care before adding new imports to clients.

        • Should be added to docs and community should be

          notified.

        • Josh/Mark: At some point will add a check to prevent

          this happening in future.

      • Review in 1-2 weeks after 5.5 build issues are fixed.

  • 5.5 Build (JM):

    • Server up and running before migration of config files.

    • Moving configuration files to the correct location has

      required more work than expected. Trying to get the server running again as quickly as possible, but anticipate tests should already pass.

    • Still need to work on Ice 3.7.

    • Hibernate issues are known unknowns, need a working build

      before investigating further.

    • Release date: unknown.

  • Iviewer (JM):

    • Remove closure is completed, PR to be merge

    • Test cleanup ongoing

    • Investigating [iviewer many

      ROIs</u>](https://github.com/openmicroscopy/design/issues/99)

    • David Egan has been highlighting OMERO, iviewer and IDR

      • https://www.linkedin.com/feed/update/urn:li:activity:6494194818455998464

  • Jason: IDR (OMERO.web) UI Updates

    • Several issues in IDR web:

      • Objects in left hand side

      • Paginations

      • Primary entrypoint: search vs browse, e.g. see online

        shops.

      • Pending design issue.

• Glencoe (Chris)

  • Updating Glencoe for 5.4.10

  • Microservices updated to support database sessions

  • Next iteration of microservices will communicate with

    Hazelcast

• Community

  • HCA: HDF call (Josh)

    • Important CxO’s showed up with alternative formats and

      alternative backends

  • Plans for OMERO Users and DevOps Training Courses (Jason/June)

    • Provisional dates:

      • Mon 8 - Tue 9 April 0830-1800 (Dalhousie)

      • Mon 10 - Tuu 11 June 0830-1800 (Dalhousie)

      • Provisionally Sep/Oct

    • Provisional plans:

      • 2 x 2 day user workshops for 15-20 attendees

      • OMERO devops sessions, but what would it include?

      • Presentations vs tutorials vs interactive workshops vs

        one-one help

    • Petr: announcement of no classical mtg?

  • Petr/JM: Visiting Singapore in March 2019

1. AOB

• Arm-friendly keyboards

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

1. Main Topic

(20-25 minutes plus 15 minutes questions max)