2017-08-15

15th August

Dundee: Will, Simon, Jason, June, Balaji, Mark, Dominik, Roger, Helen, Riad, (Jean-Marie, Seb - 14:14)

Remote: Kenny, Josh, Liza, Melissa, Eleanor, Wilma, David, Chris, Emil, Andreas

1. Accepting minutes from [last meeting](https://www-legacy.openmicroscopy.org/site/community/minutes/conference-calls/2017/2017-08-01-tuesday-team-meeting/)

1. Project Timelines (2-3 minutes each)

1. Spaces

1. [Files/Formats](https://trello.com/b/IBHfAIMP/bio-formats-5-x)/[OME Files](https://trello.com/b/WFYWCvoV/ome-files-0-4-0)

- BioFormats release. 5.6.0

- Few PRs open later today to update downstream usage

- Formats meeting this week to discuss next steps

1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata)

- IDR 4.3 plan. Data ready for releasing but a few bugs still to fix

- Could delay release or just release data but not code?

- Balaji: Notebooks - running on 30 different complexes, looking at genes wrt GO

- PR for IDR py.

1. [OMERO 5.4.0](https://trello.com/b/SiqOu2Bl/omero-540)

- Mark: Petr discovered [security vulnerability for light admins](https://trello.com/c/7xa7ggwp/111-bug-every-light-admin-can-upload-script)

- does *not* affect OMERO 5.3

- light admins could work with official scripts without `WriteScriptRepo`

- now fixed bug and adjusted the test that ought to have checked this

- Mark: performance of [deletion with heavily linked annotations](https://trello.com/c/mfW0N1an/89-poor-performance-when-deleting-many-one-annotation-links)

- severely affects IDR data management workflows

- speculative fixes did not help

- culprit: previous testing suggested Hibernate’s caching

- would like to confirm but difficult to profile server under sufficiently heavy load

- our Hibernate is several years old

- there is reason to expect better from newer Hibernate

- culprit: database trigger for reindexing

- slowest part is a fix for an even worse performance issue

- move to Elasticsearch may make trigger unnecessary

- for 5.4.0 planning a workaround

- 5.3 automatically deleting orphaned comments, etc. makes sense as a default

- find a way to extend server API to block orphan checks enough to return to 5.2 performance

- should be quite feasible

- IDR scripts could then activate workaround as needed

- Mark: [poorer server performance](https://trello.com/c/HvCCqu5z/76-db-writing-performance-testing) under concurrent write operations

- reproducible via concurrent imports or moves

- have not tested concurrent read operations

- suspicious of `_current_admin_privileges` database table

- possibly overengineered when fixing earlier issues with flakiness

- Josh is reviewing the approach

- can try again to aim for transaction-local table entries

- however, Petr found `postgres` processes not consuming much CPU

- plan to profile `ome.security.basic.*` to see if Petr missed any smoking guns

- not yet confidently identified any promising solution

- JRS: longer-term interest to upgrade Hibernate or get 5.4 out?

- Hibernate upgrade likely to take a while

- Dependent on replacing search

- Mark: re: 5.4 blockers: Certain concurrent actions can be slower in 5.4

- Might be able to reduce over-engineering in some places

- Option to add profiling to look for smoking gun

- Other

- Will: Adding tests on existing functionality

- J-m: rolling out testing devspaces

- TBC

1. [Outreach](https://trello.com/b/Da6OAWam/outreach)

- Cambridge December discussion - Gaby to start gdoc for advertising course

- 2 day course - each day independent. Day 2 advanced

- …

1. Other releases/upgrades:

1. Figure & iViewer

- ROI functionality in iViewer. Shape dimensions/stats.

- Some code might need to be moved down to server (new microservice in future)?

- FPBioimage discussion with Michael - e.g. ROI support (cropping)

1. new website

- Seb: No active changes just now

- Secvuln pages migration from old site to new

- Other content & resourses. Movies, Training etc.

- Kenny: site support url redirects. No www.legacy…

1. Sysadmin (current board and recent PRs)

- Trout re-imaging: Issues with disks. Carp (VM) to be replacement

-

1. Glencoe Update: Chris

- Masks support in OMERO.web and pathviewer

- Few existing issues. Colour mapping & display

- Also rendering and handling pngs

- Masks are ‘full image’ in use cases (very large X and Y sizes)

- Tiling of masks needed

- Rendering engine fixes to go into 5.4.0 possibly?

1. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

- Upgrade latest git etc (secvuln fix)