2010-09-14 Tuesday Meeting
Attending: Brian, Chris, Andrew, Colin, Will, Ola, Josh, Brain Jones, Scott
Agenda
Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)
Accepting minutes from last meeting
Matters Arising (<10 mins)
- Add story: Need to refactor XML Mocks so Andrew can use as samples.
- Everyone: Try to get things green again!
- Chris: Send email for server upgrade reminder
- Josh: Will send out changes to poster to nitpick list
OMERO.fs Discussion lead by Colin (45 mins)
- Where we are now
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Repository management
- Admin view
- User view
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Binary data
- Thumbnails
- Pixels
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Where we want to be
- Minimum for ASCB demo?
- Further ahead
SPIM format proposal (5 mins)
- Converted files to Guenter for apporval
- Once approved, sample file on ome-xml.org
- Need to incorporate n-dim proposal-- plan for doing this and supporting it?
- email to SPIM community
- anything else?
Monitoring Forums
- emails not working, and some events being missed
- ideas? Manual check 2x / week?
AOCB (<5 mins)
- Hotels for ASCB
Notes
Matters arising
- Holding off on XML mocks
-
Hudson green
- Remove "OMERO" job? Probably. Chris will look into it.
- Disabling the two failing python tests? May point to bugs though.
- Will will take a look at one of them to see what's up.
-
Nightshade upgrade, one big problem:
-
any changes to groups takes the server down!
- basically a database upgrade every time
- currently disabled this feature for admins (Jason)
- Chris will have to manually make any requested changes for now
- May want to note this problem in the 4.2.1 docs and web admin page
- http://trac.openmicroscopy.org.uk/omero/ticket/2872
- One other issue: import causes raw pixel store to disappear sometimes (ice not exist exception)
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any changes to groups takes the server down!
FS/Repo Talk (by Colin):
Current status
- Multi-image filesets being imported, etc. with sensible names
- Two-stage process: registration (creates OrigFile or Pixels), then metadata-only import
-
May become a single-stage process in Insight (from user perspective);
- depends on speed and value of just being "registered"
- Not currently using the "partial" flag on image
- Currently only using the test repos originally set up by Josh
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Thumbnails: Using BF thumbnails, cashing thumbnail and displaying
- No resizing, changing planes, etc.
- Do we want to change/improve thumbnailing?
Repository management
- System admin decides where files are stored?
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Users' home directories, or using some subfolder. Or will they be using a shared folder?
- Josh: These sorts of details will need thinking!
- Similar to how we needed to re-think the permissions system, the FS-level access is also quite tricky.
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What type of file-system permission models do we want to support?
- Chris: Need to plan for this in advance to avoid problems
- Josh: Have some code that starts to do this. (Sanity check on building a repo)
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Registration is a way of signalling that something can be accessed
- Currently in-place to some degree in Insight
- Not ideal in a scenario where one person acquires and one visualizes.
-
Similar to group permissions, there's a single flag ("group-based", etc.)
- That influences the repository implementation
- This is going to be like group permissions: won't know what everyone needs to start
- Colin: Per User Private seems like a reasonable starting point
- For a private repository, there must at least be a private group (possibly a special private group)
- Initially no sub-repositories
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Josh: Will probably need a repository server
- Chris: Can't just use proxies?
- This may be the time to work on the general launch functionality (cF. icegridnode)
- Need to be ready for Windows
Binary data
- Filling in the stubs is probably a good start
- Josh: The major barrier should be performance, already technically possible.
- Chris: the work on "minimal metadata" should be a good start
- CRITICAL: memory management and cleaning up BF Readers.
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Will: will need to early on create thumbnails pre- and post- registration
- Need to measure the cost of just registering all the images.
- Managing users' expectations.
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WebAdmin will need a lot of work
- If we move to another launcher framework,...
- Move things to bin/omero config
- Allow creating repositories
- etc.
For ASCB?
- What's the minimum?
- A single-repository type and render the image (may not perform the best)
SPIM
- Proposal this week? May need to hold off till Josh is back next week
- Chris: Lots of folks away for awhile as well over the next few weeks
- Andrew will email folks via nitpick for ideas
- Will: After examing Guenter's xml, there's a lot there which should be OME
- Andrew is hoping to get more sources of data
Monitoring Forums
-
Forum emails fall apart if you don't read them all the time
- Must keep on top of logging in, no other solution?
- Chris: Maybe we need a daily python script to email nitpick with new unread posts
- Chris: Need to investigate the php to see if its fixable
- For now we all must login daily
- Chris: May want to look at http://www.phpbb.com/community/viewtopic.php?f=69&t=1521515
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Forum emails fall apart if you don't read them all the time
AOCB (<5 mins)
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Hotels for ASCB
- Enough double rooms for everyone is now reserved
- We can change up to December if needed
- Anything else people need done? Should get things bought soon
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No talk this year, just a poster
- T-shirts? XKDE comic? xkcd.com/627
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Chris is looking at upgrading Agilo
- Better whiteboard, burndown fixed
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Chris is using a new java library for scaling images on trunk
- About the same speed, multi-threaded, should look better with low grade images
- Needs feedback from team/end users
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Hotels for ASCB