2011-08-11 Thursday Meeting
Attending: Brian, Ola, Will, Jean-Marie, Chris, Colin, Scott, Littlewood, Andrew, Simon, Jason, Josh, Melissa, Curtis @ 15:10, Carlos @ 14:18
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)
Andrew: Test some you tube integration with plone (for Aug 11) - done (see youtube-test-page)
Jason: Discussion about using you tube (for Aug 11) - see item below
Jean-Marie: handle FLIM stories, possibly re-assign all Donald tickets.
Jean-Marie: detail what's left to do so we can adjust the timeline
-- Following points made from minutes
Brian has made nice memory doc on trac; #6388;
- reply to Forum post;
- move to OMERO clients on om.org
Jason: write again to PE.
Ola to do PSLID this week
Jason: Email Andrew & Ola about furniture for CTIR.
PyTables testing-- Josh? Simon? Carry Forward.
Scott: Ask Paul Felts about cost of scanning Done - Jason confirmed we can help
Chris: Tickets for "What to do about Agilo? and git?"
Presentation of FS (10 mins)
Glencoe Update
Status of 4.3.2 Milestone
Minigroup Updates
- HIC
- Model
- FS
- Web
Using You Tube to promote OME (5 mins)
Email and Forum Review - checked at 10:20 (5 mins)
Email -
- Leon Kolchinsky [ome-users] Problem running omero configuration
- Jacques Pécréaux [ome-users] frequent and unexpected deconnexion of clients from server
- Ghislain Bonamy [ome-devel] Eclipse metadata in bio-formats.git
Forums -
QA -
linkID Status User/email Type Created Selected file Comment Error 3924 new rpalmisano@u... Importer 4.3.1-6d4b 2011 08 10 harris.tif - java.lang.NullPointerExce... 3923 new lem@stowers.... Insight 4.3.0 2011 08 09 - - java.lang.Exception: java... 3921 new S.C.Moser@du... Insight 4.3.1 2011 08 05 - hi guys, it can't import some ... - 3920 new S.C.Moser@du... Insight 4.3-DEV 2011 08 05 - Hi guys, there is a bug today ... - 3913 new unknown Insight 4.3.1 2011 08 02 - Loading a new set of ROIs to a... java.lang.Exception: Abno... 3912 new r.disanto@du... Insight 4.3.1 2011 08 02 - - java.lang.Exception: Abno...
Any other business (<10 mins)
- Scott: Training update dates confirmed 3rd and 4th of October - I need 2 developers with the experience of OMERO scripting to help with running of the scripting day. Confirm mini group meeting for those involved.
- Vcell Bio-Formats license
Notes
Attending
- Brian, Ola, Will, Jean-Marie, Chris, Colin, Scott, Littlewood, Andrew, Simon, Jason, Josh, Melissa, Curtis @ 15:10, Carlos @ 14:18
Notes
Accepting minutes from last meeting
Matters Arising (<10 mins)
- Andrew: Test some you tube integration with plone (for Aug 11) - done (see youtube-test-page)
- Jason: Discussion about using you tube (for Aug 11) - see item below
-
Jean-Marie: handle FLIM stories, possibly re-assign all Donald tickets. - IN PROGRESS
- Needs to merge code
- Jean-Marie: detail what's left to do so we can adjust the timeline - IN PROGRESS
-
Brian has made nice memory doc on trac; #6388;
- reply to Forum post;
- move to OMERO clients on om.org
- Some way to link into clients page on o.org
- Brian: easy to move over; will respond to 6388
- Jason: write again to PE. DONE
-
Ola to do PSLID this week
- Not done. Sure if this can be done before next meeting. (Ola busy with other tasks so will have to wait)
- Move this to web meeting.
-
Josh: There is a branch on team with all their changes so we can see what's changed
- Josh: We should let them know the best format for providing us code
-
Ola: Can we do this next sprint? Josh: Should be fine
- Ola can do the basic work next Monday/Tuesday for them
-
Jason: Can we just give it a preliminary look and get back to them with feedback?
- Chris: Can do it, but will need to have it done before next Wednesday (travelling on the 17th)
- Ola: then review on Tuesday web meeting.
- Jason: Email Andrew & Ola about furniture for CTIR. - DONE
-
PyTables testing on OME resources IN PROGRESS
-
Old maintainer has left, donated commercial code under BSD license
- Installers and indexing are now open source
- Josh: Do we continue to use this? Any licensing issues if we run tests on our box?
- Jason: We should stay with PyTables for awhile since we have investment here
-
Andrew: Is this internal only testing? Josh: Lots of new coded added to PyTables that needs testing
- Jason: Since we need it, lets add testing for it
- Josh: After getting off git hub, (we would do this something like nightly) very extensive test suite is already there for testing
-
Old maintainer has left, donated commercial code under BSD license
-
Scott: Ask Paul Felts about cost of scanning DONE - Jason confirmed we can help
- Another application for a relatively small investment
- 50 slides for pathology students.
-
Will: Is lack of ROI on big images a blocker for him? Scott: Eventually it will be
- Jean-Marie: what's the issue?
- Scott: roi for annotation
- That could be the first step.
-
Chris: Tickets for "What to do about Agilo? and git?" (@ 15:18)
- Chris: Perhaps more sensible to have that as a Tuesday meeting.
-
Will: Do they require everyone? Do they require a presentation?
- Chris: yes on both accounts.
- Ola: any discussion by email before hand? so people can get familiar
-
Will: looked briefly at list, thinking about which ones to discuss
- No dedicated person for most of the topics
- Nor a clear "WHEN"
- Scott as the next one?
- Will: someone will need to take over the list for the next several weeks.
Presentation of FS (10 mins)
-
Colin: need to handle files which bio-formats does not pick up
- folder full of DVs, with one non-imported file; what if that gets deleted.
- if we just copy them, how do we display those to user? just tell them to go to /OMERO/Repo...
- Jason: if I see 2 filesystem views, and they're different, I'll be unhappy.
-
Will: you have to be able to browse everything that was originally there
- even if not attached, not annotations.
-
Jason: semantics of terms like "archived"
- Colin: probably just a by-product of re-using the "archiving" functionality
- Colin: do we still need the id in the path?
-
Jason: conflating the requirements.
-
Melissa: 2 cases
- Thumbnails ignored on usedFile list
- Put on usedFile list as part of the dataset, but ignored by the reader
- Jason: as user, let me be dumb
-
Melissa: 2 cases
-
Jason: don't be too smart
- Chris: tension between 2 points
-
If I do an archive and directory structure is different, I'm going to raise the flag that something is wrong.
- i.e. we can detect what files are in what sets
- More difficult, though, to understand what other files if you want automated set
-
Jason: tell me "click on the XML file"
- ...
-
Josh: for the goal of de-duplication
- either have to move all the files
- or let bio-formats/insight delete the transferred ones.
-
Will: don't like either of those options
- prefer dropbox like
- transfer all the files, i can look at them and then delete them locally.
-
Chris: that's the tension between how we currently import and just copy it all to the server.
- Clients just become a dumb copy
-
Andrew: now the directory is nice and browsable
- How to we prevent people from messing with them?
- Chris: not an investigation of that
- Josh: documentation says make it unreadable
-
Will: why do you have to configuration directory path?
- why can't users put things where they want?
- Chris: for the moment, you need some form of prefix
- Colin: maybe user configurable
-
Chris: base-admin template, because they need some structure (like /DropBox)
- for quotas per lab or whatever
-
Jason: ok, how long?
-
4116 is pretty big.
- See Curtis' proposal
- Could spend some time on metadata levels
- ...
-
4116 is pretty big.
-
Colin: need to handle files which bio-formats does not pick up
Glencoe Update
- HCS coming along
- opposition to trademark
Minigroup Updates
- FS: see above.
-
HIC
- Simon: Met with Andy/Alison about governance of HIC datasets. New Tickets with XML schemas about this
- Also added an information page on the wiki with info on governance arenas
- Josh: trying to find small, reusable components that we can re-use elsewhere
-
Model
- Andrew finishing off transforms
- Next week: restructuring of test directories
- Will be looking for input from Josh next week on this
- Have looked at the HIC data
-
Chris: integration point examples
- 3/4 of that webpage is written
- what you should and shouldn't do
- and what you can do ("but please contact us first")
- All points listed on the milestone page
-
JMB: closing ome-xml.org?
- wiki is still there
- need to be copied over.
-
Curtis email about broken links?
- Replied privately.
-
Web (@ 15:30)
- lots of incoming changes to SPW (merging Carlos' plugin)
- gateway: adding scripting functionality
-
changes for extension infrastructure
- Chris modified the decorators to prepare the base, what people should use
Status of 4.3.2 Milestone
- Jean-Marie: initially were going to do bug fixes like 4.3.1
- Chris: original closing date was Aug. 31st.
- Andrew: weren't we talking about end of September
-
Jean-Marie: should go through later and pick out the high priority
- some of the tickets may not need to be here
- Jason: need a full review.
- Josh: 40+ bugs
-
Josh: open quesiton what are the next buckets and their deadlines.
- Jason: less an issue of particular dates
- for next few months (end of this year) it's about fixing big things: chgrp, fs
- things that people rate as "blocker"
-
Scott: what about the Paris list.
- Jason: 4.3+ priorities is a pretty good statement of
- Jean-Marie: chgrp is 4.4 (changes to the server)
- Josh: I'd be careful about a 4.3.3 if we want to take on some of the blockers.
-
Jason: drifting...
- Next thing that needs to happen is the audit
- Including web, FLIM, formats, model, etc.
- Audit them over the next day or two.
- Chris: today and tomorrow are the only days for August where all of us are here.
- Andrew: model meeting with Jason.
Using You Tube to promote OME (5 mins)
- Quality is low; Andrew couldn't make it not look fuzzy.
-
If you don't use an iframe, then it will only work on 2 of 4 browsers
- Will never work on all of them.
- If it looks crap, we're not doing it.
Email and Forum Review - checked at 10:20 (5 mins) @ 13:45
Email -
- Leon Kolchinsky [ome-users] Problem running omero configuration
- Jacques Pécréaux [ome-users] frequent and unexpected deconnexion of clients from server
- Ghislain Bonamy [ome-devel] Eclipse metadata in bio-formats.git
Forums -
-
Re: Out-of-bounds ROI creation
- Chris & Will: have discussed that we've always allowed it
- No good way to prevent it.
- Linking to additional ontologies
-
Re: Out-of-bounds ROI creation
QA -
link3924 new rpalmisano@u... Importer 4.3.1-6d4b 2011 08 10 harris.tif - java.lang.NullPointerExce... 3923 new lem@stowers.... Insight 4.3.0 2011 08 09 - - java.lang.Exception: java... 3921 new S.C.Moser@du... Insight 4.3.1 2011 08 05 - hi guys, it can't import some ... - 3920 new S.C.Moser@du... Insight 4.3-DEV 2011 08 05 - Hi guys, there is a bug today ... - 3913 new unknown Insight 4.3.1 2011 08 02 - Loading a new set of ROIs to a... java.lang.Exception: Abno... 3912 new r.disanto@du... Insight 4.3.1 2011 08 02 - - java.lang.Exception: Abno...
Any other business (<10 mins)
-
Scott: Training update dates confirmed 3rd and 4th of October
- Need 2 developers with the experience of OMERO scripting to help with running of the scripting day.
- Confirm mini group meeting for those involved.
-
Notes
- Go down for a couple of days
- Slightly different from JIC
- Second day is more focused (scripting)
- Need to explore more how he's wanting that setup
- Dev offer: Ola?
-
Vcell Bio-Formats license @ 13:54
- See nitpick email thread
-
Scott: Training update dates confirmed 3rd and 4th of October
Action Items
- Brian: Move over client memory doc to om.org, let Jason know so he can send email
- Chris: Look over PSLID codde and provide feedback. Ola can review with you on Tuesday.
- Andrew: add git, etc. points to Tuesday meetings.
- Chris: upgrade nightshade to 4.3.1
- Everyone: tomorrow (Friday) is ticket review!!!
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2011-08-09 Tuesday Meeting
