2017-01-17 Tuesday Team Meeting
Dundee: Kenny, Petr, Mark, Dominik, Jean-Marie, Jason, Ola, Simon, June, Will, Simone, Roger Remote: Sebastien, Josh M, Helen, Eleanor, Melissa, Emil, David, Wilma
Agenda - 2:00pm Start
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
Spaces - 14:00 UK
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Files/Formats/OME Files (Sebastien)
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OME Files 0.3.3
- first part of the proposed model extension integrated
- next step will be API addition for creating model objects and registering custom types (e.g. Annotation of type csv, modulo….)
- Also initiated work on Python bindings for OME Files C++ in the perspective of CMSO meeting at the end of the month
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OME Files 0.2.3
- generally positive reviews on the submitted paper
- Major requirement are data supporting our “performance” statement.
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initiated work on measuring performance of OME-TIFF reading/writing using C++/Java
- Roger: now mostly done, should have comparison before going on leave
- Jason: modern acquisition systems so complex and varied that map annotations may be the way forward in modeling them
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Bio-Formats 5.3.x
- ongoing improvements/bug fixes for the TIFF writing functionalities including review/expansion of the test coverage
- proprietary file formats improvements coming from Glencoe and external (Michael Golzer from Leica)
- preparation of the testing of ome-model 5.4.0: import/export of transforms in Bio-Formats & OMERO
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OME Files 0.3.3
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Metadata (Josh)
- 0.3.2 going out tomorrow (barring disaster) incl. idr0032
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0.3.3 will likely focus on populate metadata extraction
- pip installable, targeted annotation deletion (namespace)
- Eleanor: hoping to get a couple more datasets in
- https://trello.com/b/gitlBfRQ/idr-0-3-3 cleanup needed
- will in due course need more Bio-Formats help
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OMERO 5.3.0 (J-M)
- 5.3.0-m7 tagged yesterday
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Possible DB change
- soon finalizing 5.3 DB
- may be of particular interest to Glencoe
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Web API
- Will: adding URLs for browsing JSON data (navigation, etc.)
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New Role
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Mark: current plan is,
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this week: split WriteFile privilege out separately for WriteOfficialScript, also Write privileges out from Delete privileges
- map OriginalFile.repo into OMERO object model but prohibit changing it
- next week: focus on on user management privileges: create group, add to group, etc.
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after that work, main remaining themes for 5.3.0 are:
- block privilege elevation routes, e.g., add friend to system group
- provide IObject.can* methods so clients know user's powers
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probably push into 5.3.x:
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import into other groups
- some of the new roles integration tests rely on this and would thus be broken in the interim
- client UI work
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import into other groups
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probably push beyond 5.3.x:
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restrictions such that user's powers are even less than that of the user to whom they sudo'd
- e.g., sudo to a normal user to import for them but then cannot delete their data
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retention of privileges even after sudo'ing to less powerful user
- possibly a bad idea anyway
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restrictions such that user's powers are even less than that of the user to whom they sudo'd
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this week: split WriteFile privilege out separately for WriteOfficialScript, also Write privileges out from Delete privileges
- Mark: given availability from others, could at short notice hand off writing of integration tests
- Jason: is reasonable to expect some intelligence and responsibility from users
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Mark: current plan is,
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Outreach
- Jean-Marie: people off to Texas
- Jean-Marie: need to fix a date for summer training in Cambridge
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Files/Formats/OME Files (Sebastien)
Other releases/upgrades - 14:22 UK
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Figure
- "compiled" code no longer on gh
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iviewer
- "compiled" code no longer on gh
- Learning
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Sysadmin
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Josh: Ansible/Galaxy strategy (social media coming)
- following restructuring PR only playbooks in repository, your roles should be off in other repositories
- Kenny: demo server isn't allowing saving tags
- to discuss plans for nightshade
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Josh: Ansible/Galaxy strategy (social media coming)
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Website redevelopment/redesign (Liza)
- no update until mid-February
- Smuggler (Montpellier)
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Figure
Glencoe Update (Chris) - 14:28 UK
- working with opensource web team to get PRs merged
- mostly fixed issues with TIFF writing, outstanding issues with many-channel BigTIFF
- work on read-only server infrastructure
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 14:30 UK
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OMERO code issues reported by AppChecker
- Jean-Marie: list a couple in each standup
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OMERO code issues reported by AppChecker
Jason year overview (20-25 minutes plus 15 mins questions) - 14:32 UK
- comments welcome
Done 15:42 UK