2017-08-15-tuesday-team-meeting
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
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
Spaces
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- BioFormats release. 5.6.0
- Few PRs open later today to update downstream usage
Formats meeting this week to discuss next steps
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- 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.
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Mark: Petr discovered security vulnerability for light admins
- does not affect OMERO 5.3
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light admins could work with official scripts without
WriteScriptRepo
- now fixed bug and adjusted the test that ought to have checked this
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Mark: performance of deletion with heavily linked annotations
- severely affects IDR data management workflows
- speculative fixes did not help
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culprit: previous testing suggested Hibernate's caching
- would like to confirm but difficult to profile server under sufficiently heavy load
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our Hibernate is several years old
- there is reason to expect better from newer Hibernate
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culprit: database trigger for reindexing
- slowest part is a fix for an even worse performance issue
- move to Elasticsearch may make trigger unnecessary
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for 5.4.0 planning a workaround
- 5.3 automatically deleting orphaned comments, etc. makes sense as a default
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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
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Mark: poorer server performance under concurrent write operations
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reproducible via concurrent imports or moves
- have not tested concurrent read operations
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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
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however, Petr found
postgres
processes not consuming much CPU
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plan to profile
ome.security.basic.*
to see if Petr missed any smoking guns - not yet confidently identified any promising solution
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reproducible via concurrent imports or moves
- JRS: longer-term interest to upgrade Hibernate or get 5.4 out?
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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
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Other
- Will: Adding tests on existing functionality
- J-m: rolling out testing devspaces
- TBC
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Mark: Petr discovered security vulnerability for light admins
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- Cambridge December discussion - Gabriella to start gdoc for advertising course
- 2 day course - each day independent. Day 2 advanced
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Other releases/upgrades:
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)
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...
Sysadmin (current board and recent PRs)
- Trout re-imaging: Issues with disks. Carp (VM) to be replacement
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?
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - Upgrade latest git etc (secvuln fix)