2024-04-30

Attending: Will, Dom, JM, Petr, Andreas, Frances, June, Josh, Kevin, Khaled, David, Erin, David S, Kyle, Melissa, Seb, Chris, Maadhav,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each) Brief report 15mins max for all.

• IDR (Frances)
  • prod121 release tomorrow idr0157 large plant study
  • also includes rocky9 upgrades
  • will deploy fresh idr-testing after release for final round of NGFF testing
• OMERO
  • Working on nightshade migration to Rocky 9
  • Web PRs in progress, close to merging
• Bio-Formats
  • ZarrReader PR in review, then tag and release for IDR
  • Flex PR (idr0001) assess scope of fix needed
• NGFF
  • https://forum.image.sc/t/ome-ngff-update-postponing-transforms-previously-v0-5/95617
  • https://github.com/ome/ngff/pull/227
  • Zarr v3 RFC PR to be merged and e-mail reviewers soon.
  • FYI https://github.com/AllenNeuralDynamics/jomezarr
• GerBI
  • writing papers: promote data management and funding for it
• Glencoe
  • JSONp discussion, deprecation?
  • Erin: recent meetings: ACR, BioIT, ABRF, https://aacrjournals.org/cancerres/article/84/6_Supplement/4933/736512
    • Upcoming Janelia blog on formats
• Community
  • June: meeting registrations picking up
  • Monday: OME team (Dundee) day off

AOB

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

Main Topic

Technical discussion focusing on Java version 17 suupport in OMERO.server

• Feedback on process welcome
• Java programming language - LTS releases
• Core OME repos in Java. Require Java 8+, Some Java 11
• Users need JRE to run apps
• Devs need JDK - OpenJDK released 2007 by Sun Microsystems
• Now multiple JDK distributions
• JDK builds only get support for 6 months
• Other vendors ship their own OpenJKD releases with different EOL
  • e.g. RedHat JDK 11 EOL Oct 2024
• Bio-Formats 6.12.0 added support for Java 17
  • recently added support for Java 21
• OMERO server doesn’t yet support Java 17 - reflection issue
  • Strongly encapsulated - can’t access protected/private Java API methods
  • workaround: use –add-opens to JVM
  • also need –add-exports to avoid IllegalAccessError
  • This allows us to run OMERO.server on Java 17
  • These options not supported for Java 8.
• Next steps:
  • review dependencies etc to remove need for reflection