2015-12-01 Tuesday Team Meeting
Dundee: Dominik, Kenny, Petr, Mark C, Jean-Marie, Simone, Will, Gus, June, Helen, Roger, Balaji Remote: Sebastien B, Kelli, Colin, David, Wilma, Melissa, Ian, Curtis
Agenda - 2:30pm Start
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
OMERO - 14:30 UK
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5.2.1 (J-m)
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starting to clean up the documentation, including Windows and web deployment
- alternative to SCL on CentOS 6
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nightshade upgrade revealed problems
- Kenny: added to nightshade card
- Jean-Marie: link from deployment column
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Kenny/Will: e-mail to warn people?
- Helen: already told CentOS 6 people to hold off for now
- also WSGI / Apache issue
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may need troubleshooting page for our documentation
- Roger: already a CentOS 6 page
- Kenny: issue needs to be more obvious from sysadmin upgrade page
- some PRs open, was focusing on deployment issues before merging further changes
- Mac OS X docs have been taking shape
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starting to clean up the documentation, including Windows and web deployment
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Metadata
- Colin: with Simon now rebasing PRs from metadata to develop
- Simone: working on metadata Python repository (idr-metadata repo, Josh M has been trying it out), driven by MULTIMOT work
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5.2.1 (J-m)
Bio-Formats - 14:39 UK
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5.1.7 (Melissa)
- now under PR freeze
- need to make jobs green so may have to push release date to Monday
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5.2.0
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Folders
- Mark: Start with a Folder that can contain just ROIs, maybe Images? Or a Folder that can contain any top-level object, or maybe exclude Screen, Project, Dataset from that? Comments welcome on ROI Folders.
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general consensus seems okay with starting with just ROIs and Images as Folder contents
- Jean-Marie: risk of including too much too soon and having it misused
- Mark: slowed down by unexpected code generation issues on both Bio-Formats (recursive elements) and OMERO (significant ordering), and by the merging of regions into develop on Bio-Formats, but will be able to push branches by the end of the week if nothing else
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Roger: Mask and BinData generation progress?
- David: coming along, still some to-do’s
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Folders
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5.1.7 (Melissa)
Other releases/upgrades: - 14:51 UK
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Figure
- Will: now released, could look at release process improvements
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Kenny: mention Pillow version on install instructions?
- Will: absolutely, but is probably a more general OMERO scripts issue than just Figure
- Jean-Marie: in longer term could improve testing to catch these issues
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FLIMfit/OPT (Ian)
- I'm now working on upgrading the Localization Microscopy work to be compatible with 5.2.
- demonstrating next Tuesday
- IDR Project
- ImageJ
- Learning
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Sysadmin (Kenny)
- nightshade is back on its feet and users can log in
- a few files seem corrupt, but appear to have been that way for a long time, will investigate
- PostgreSQL indexes rebuilt
- Chris suggests providing post-mortem details in a blog post (using import logs, checksums in DB, etc.)
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Jean-Marie: black thumbnails?
- Kenny/Gus: nothing further known
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Petr: some still exist on nightshade
- Jean-Marie: sent out e-mail with workaround
- Petr: there could be an easier way for users to regenerate thumbnails in bulk
- Roger: also pyramids
- Roger: server probably still doesn’t requeue aborted jobs on restart
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Figure
Glencoe Update (Wilma) - 15:01 UK
- webinar just started
- attending digital pathology meeting at end of week
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:03 UK
- June: David and Jason off to workshop in Cambridge next week, Simon to attend light microscopy managers’ meeting
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Simone: anything about signing up for MULTIMOT meeting in March?
- June: will find out
- June: still waiting for plenty of OSAR forms back
Done 15:05 UK