2010-03-09 Tuesday Meeting
Attending: Brian, Jason, Donald, Ola, Will, Jean-Marie, Colin, Melissa, Carlos, Josh, Chris, Scott, Andrew
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 - No actions for today
File System: Jean-Marie & Colin's presentation (45 mins)
AOCB (<5 mins)
- Microscopy Image Analysis for Biomedical Applications - One Day BMVA technical meeting in London, UK, on 21st April 2010
Notes
Accepting minutes: nothing for today (all for Thurs.)
Matters arising
-
Permissions testing phase II
- Will sent feedback
- @Jean-Marie and Ola need to synchronize some insight/web issues
- also need to gather various things which are disallowed (usability)
- and then integrate that into security system
-
thumbnail overhaul
- Chris: important to try wacky things
- "go to someone else's image"
- goal: make sure you don't get someone else's views
- @everyone will need to import data into mage
- @look out for issues in BOTH web and insight
-
Which importer build to use? (Jason)
- No changes made. You will always get your default group.
- Or you can import from Insight. DON'T
- But not from OS X .... BUG!
- @Brian makes a QA build
-
Warlock / HCS_PREVIEW
- Preview build is crashing
- Downloaded from download page
- Linked version seems to be broken.
- @Fix Hcs preview page
-
ticket:1855 (4.1) - session timeouts
- @send an email to ome-devel
- Josh will commit to trunk for testing.
-
FAQ
- @Should be done by Thursday
-
Permissions testing phase II
Demo server statistics (Ola)
- no real feedback from any of the demo users
- ~300 images. mostly OIF and tiff. also jpeg, lsm, ...
- mostly PD, some few screens
-
opinion: mostly looks like people are testing import
- some examples of import failing
- @How many bugs came from demo accounts?
- Jean-Marie: would be interesting to ask what people are importing
- Chris: maybe they aren't sending feedback?
-
@Could we get the list of terms? (possibly pre-defined values)
- Ola: mostly "test", "test1", ...
- 36 accounts. 12 imported something. (excl. our & KIT accounts)
-
Chris: can we find why 2/3 didn't import? cF. logging in.
- Jason: do we then offer to get some data in for them
- Ola: shouldn't be so hard to send an email
NB: be sure to update the agenda if you want to talk so external folks know
OMERO.fs status
- user acceptance: users are familiar with their file system; makes life simpler for them
- fs returns which images are import candidates
- local filesystem? no, it's the server file system
- an image gets registered with the server as soon as you try to say something (happens automatically)
-
thumbnails generated on the fly for the files which are relevant to you (even when unregistered)
- No settings interaction with the generated thumbnails
- The thumbnails get generated for use later
- Josh: @we'll need to decide how to handle the same hierarchy for multiple users / groups
- Jean-Marie: needs to be as smooth as possible
-
Colin: repository is a public API
- can only view into the repository
- currently registering importable files as "Image" and other as OriginalFile.
- How much information needs to go into the OriginalFile to be useful for the user?
-
Very crude thumbnail holding system
- cached on local filesystem
- Nothing pre-emptive; directory with 1000 files could take a file
-
format
- need is to do OS-based "Open with ..." functionality
- currently using mimetype (everything octet-stream)
-
next phase
- address issue of files with multiple parts (LIF)
- deregistering objects
- @adjustment to importer to pass the original file id for linking
- @adjustment to server for better identifying files which have been registered as file and/or image
-
How much should we associate with the image without a full import?
- Chris: perhaps we can start with metadata only imports (performance?)
-
future API
- methods exist for getting existing services. should we use them?
- file services necessary -- copy/rename files, etc?
- where does monitoring come into play? (watching for moves/deletes/etc.)
-
biggest problem is non-UNIQUE for original file
- Josh: plan is along the lines of UNIQUE (path, repo_url, group_id)
-
Jean-Marie: would like to get to the point of importing data for Paris
- But likely don't want to do this work for May release
- Need to handle security issues
- Still a long way to go, but we can go to Paris with a good list of questions
-
User wants it all (Jason)
- easy, movable, see what I want
- Balancing act: when is an image in OMERO and when isn't it
- Overriding issue: we've worked through server-fs visible, but data duplication isn't solved
-
Chris: data duplication is easy to solve
- once this interaction (exchange of files, registration, display etc.) is settled
- the rest is done (bioformats can already read from the fs)
- Jean-Marie: adjustments that you get data at a reasonable speed
- Jason: suspect the thing to do is go after the data dupe solution * i.e. focus on the partial (metadata-only) import * while keeping caveats in mind * Chris: warning for sysadmins (ldap, fs, etc.) * Chris: will soon start reviewing bioformats for getting access to binary data with metadata
-
Thumbnail location
- local v. remote
- using extended attributes for recognizing files
BMVA (21.Apr)
- OME has been invited to present
- we've missed several other invitations
- @Jason will respond, confirm, and say contact Donald (abstract end of this week)
Tickets
- Update the workplan pages. Bring deviations to everyone's attention
-
Some work to do for FLIM ("Flim integration"). Assigned to iteration. Positive feedback.
- Curve fitting time may go up to 20 minutes. @Discuss with David
- @Donald moves Flim work to requirement, and links in Stories and Tasks
- NDim workplan page is linked off the roadmap page
-
NoSQL meeting
- interacting with compsci community
- keeping an eye open for what's going
- what else would be interesting? (DB, OpenGL, Java, ...)
Action Items
* Jean-Marie & Ola: synchronize some of the permission insight/web issues
* Everyone: import data into mage, then look for issues in BOTH web and insight
* Brian: make a QA build of the importer for everyone to use
* Someone: Fix the HCS preview page (Josh? Andrew? Chris?)
* Josh: Send an email to ome-devel re: ticket #1855 (session timeouts)
* Everyone: ALL FAQ QAs should be done by Thursday
* Ola: follow up with demo users about what they were doing (why were they creating lots of empty containers). Find out how many bugs were generated from demo users.
* Ola: Check the sessions table to see how many of the demo users actually logged in.
* Chris/Brian: adjust the importer to pass original file id for linking
* Josh: organizes a discussion on ofiles [UNIQUENESS(https://trac.openmicroscopy.org.uk/omero/ticket/1753)
* Josh: we'll need to decide how to handle the same hierarchy for multiple users / groups
* Jason: respond/confirm presentation for Donald @ BMVA
* Everyone: Update your workplan pages for anything new and let folks know
* Donald: move FLIM work to requirements and link in stories and taks
* Everyone: Any suggestions for NDim workplan please let Donald know