2011-11-22 Tuesday Meeting
Attending: Jason, Will, Colin, Scott, Andrew, Josh (notes), Chris, Mark, Melissa, Ola (joined 14:35 UK; notes), Carlos (joined 14:39 UK), Curtis (joined 14:40 UK)
Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)
Housekeeping Pre-Meeting - 2pm Start
Matters Arising (<10 mins)
- Josh: ask Chris about VirtualHost - done
- Ola: link ticket to Alex’s QA or create new ones done
- Will: ask for timings on SVS files done #7298
- Andrew: cleanup google docs and define organization - done
- Will: look at using includes for the training inclusion - ome-xsd browser
- Andrew: ask Andrew about drupal - Site created by Andrew Millar for us to trial - done
- Trainers: trying training docs under sphinx
- Andrew: get Davey on the website - Davey asked to call in for photo by Jason
Email and Forum Review - checked at (5 mins)
Email -
- Leon Kolchinsky - Re: [ome-users] SVS file format functionality problem
Forums -
-
Code forum review
- OMERO.Scripts Restore Colors link
-
Code forum review
QA -
linkID Status User/email Type Created Selected file Comment Error 4047 new i.porter@lif... Insight 4.3.3 2011 11 21 - When using the paste setting o... - 4046 new a.nicolas@du... Insight 4.3.3 2011 11 21 - A few suggestions: - When impo... - 4045 new k.j.z.hands@... Insight 4.3.3 2011 11 17 - opening a screening image from... java.lang.Exception: org.... 4044 new k.j.z.hands@... Insight 4.3.3 2011 11 16 - opening an image from a screen... java.lang.Exception: org.... 4043 new a.herbert@su... Web 4.3.3-00d1 2011 11 14 - I had logged on to look at a n... Traceback (most recent ca... 4038 new CJW@stowers.... Insight 4.3.3 2011 11 10 - I am getting a "no processor a... -
Agenda - 2:30pm Start
Accepting minutes from last meeting
Movie audit: Colin's presentation (20 mins)
Sprint Status / Branches
-
Proposed for merge-blue
- PR 31 / Ice3.4: Branch has been initially tested, but this is obviously a very large change that will need large scale reviewing.
- PR 30 / insight build
- Others?
-
Next?
- Hibernate 3.5
-
Proposed for merge-blue
Glencoe Update
Minigroup Updates
- HIC
- Model
- Web
- FS
- Usability
Satellite Update
- "New" Satellites
Java 1.6 (in context of netCDF), see email to nitpick
Encoding 2-d plane information in a URL (from Lee Kamentsky)
Licensing for SCIFIO and OME-XML components (see email to nitpick)
- Latest version from offline discussion btwn Jason, Kevin & Curtis
Hiring
Any other business (<5 mins)
- PRs & screenshots/movies
-
Advertising Docs
- Our own?
- Monash docs ?
- Use of OMERO by CLS-- a usability project?
Attending
* Jason, Will, Colin, Scott, Andrew, Josh (notes), Chris, Mark, Melissa, Ola (joined 14:35 UK; notes), Carlos (joined 14:39 UK), Curtis (joined 14:40 UK)
Housekeeping Pre-Meeting - 2pm Start
Matters Arising (<10 mins) Started at 14:03 UK
- Josh: ask Chris about VirtualHost - done
- Ola: link ticket to Alex’s QA or create new ones done
- Will: ask for timings on SVS files done #7298
- Andrew: cleanup google docs and define organization - done
-
Will: look at using includes for the training inclusion - ome-xsd browser
- Haven’t looked into trac includes. Perhaps wait on sphinx.
- some work done on ome-xsd
- Andrew: ask Andrew about drupal - Site created by Andrew Millar for us to trial - done
- Trainers: trying training docs under sphinx PENDING
- Andrew: get Davey on the website - Davey asked to call in for photo by Jason IN-PROGRESS
Email and Forum Review - checked at (5 mins)
Email -
-
Leon Kolchinsky - Re: [ome-users] SVS file format functionality problem
- See ticket 7298 above.
- Chris and Will to define a response.
-
Leon Kolchinsky - Re: [ome-users] SVS file format functionality problem
Forums -
-
Code forum review
-
OMERO.Scripts Restore Colors link
- Andrew to request the script
-
OMERO.Scripts Restore Colors link
-
Code forum review
QA -
linkID Status User/email Type Created Selected file Comment Error 4046 (SCOTT) new a.nicolas@du... Insight 4.3.3 2011 11 21 - A few suggestions: - When impo... - 4047 (JM) new i.porter@lif... Insight 4.3.3 2011 11 21 - When using the paste setting o... - 4045 (JM) new k.j.z.hands@... Insight 4.3.3 2011 11 17 - opening a screening image from... java.lang.Exception: org.... 4044 (JM) new k.j.z.hands@... Insight 4.3.3 2011 11 16 - opening an image from a screen... java.lang.Exception: org.... 4043 (JM) new a.herbert@su... Web 4.3.3-00d1 2011 11 14 - I had logged on to look at a n... Traceback (most recent ca... 4038 (JM) new CJW@stowers.... Insight 4.3.3 2011 11 10 - I am getting a "no processor a... -
Done at 14:23 UK
Agenda - 2:30pm Start
Accepting minutes from last meeting Started at 14:30UK
- done
Movie audit: Colin's presentation (20 mins) Started at 14:32 UK
Colin: Question from Jean-Marie some time ago
Jason: Not just movies on filesystem, but linked to from somewhere
- Andrew: generated list of movies linked
Andrew has tried to support Windows, but no Linux.
Chris/Jason: all movies before 4.x; none after
Colin: Where else we could use movie? For example, training support. We could also identify training materials and bring up some on-line learning movies.
Colin: When we suppose to make movies? Major release, any point of the release, implementation, testing,...
Colin: Who will make movies? do we want to have dedicated person/team who will make a movie?
Colin: Ready-to-use environment would be useful to make movies. People do not want to spend couple of hours to import images, etc.
Colin: Movie content review:
- Introduction: everyone say ‘hello’ and introduce who the person is.
- Some time there is reference to other movies, we shouldn’t do it because is difficult to keep track of which movie author refer to.
- Cleaning db. We should avoid fake entries in environment we use for movie, especially testing entries.
- We need to make sure client/webbrowser window fully fit into the screen.
- We need to make sure there are no noises behind.
- It is nice to see mix of web browsers and OSes.
Jason: IE users hit our website the most.
Andrew: I was making movie with capturing entire Windows VM desktop. It looks nice.
Jason: Comments on numbers. Support people to make movies? But remaking 50 movies is still a lot of work. Maintenance is a huge burden.
Will: we have got movies which cover couple of features and some which demonstrate just one thing. I was wondering if your playlist is just another way of organizing them. I guess that sort of type of organization might help with the new release, where we will be able to review what should be recaptured.
Josh/Will: just use youtube? Allow people to discover other films.
Andrew: it would be nice if we can make youtube-style while you go to end of the movie. If we start using Drupal it will make more sense to find decent media plugin to do it.
Jason: We need movie_details file and identify what needs to be redone.
Jason: your impression that the pre-4.3 were hopelessly out of date? Colin: no.
Need to manage the original files better
Andrew: currently we have them on squig
Scott: Might be useful to have some of those movies for testing process.
Jason: my impression certainly find bugs but it shouldn’t be done for testing process.
- Colin: there is not problem with making scenario for the movie, which potentially help testing.
- Jason: how do we standardise databases for making movies?
Summary to be turned into tickets:
- DB setup
- Scenarios
- Management of original files
- All files in one place (youtube?)
- Colin’s other points.
Done at 15:06 UK
Sprint Status / Branches
-
Proposed for merge-blue
- PR 31 / Ice3.4: Branch has been initially tested, but this is obviously a very large change that will need large scale reviewing. * Josh: time scale depends how long does it take to test it. Ice 3.4 unfortunatly touch everything. We need to retest everything.
-
PR 30 / insight build
- Will: Does it make sense to have 2 branches: ‘develop’ and ‘everything else’.
- Josh: We haven’t fully tested. It will make potential problems if we merge with develop.
- Will: I am not sure how difficult would be making development in my branches and test occasionally it on ‘server’ (not sure that sentence - ola)
- Chris: If there is anything broken in ‘develop’ there is no way to roll-back. Effectively everyone is blocked then waiting. We could potentially dedicate few people test work as we go.
- Josh: I would feel safer.
- Josh: this is the issue with branches which effect the full stack. Have to have a way to do it?
- Will: I am curios if I could download server pack form Hudson and install Ice 3.4 and got from there insteand of merging.
- Josh: I have a script for Homebrew to do it.
- Chris: how many are using homebrew? Will, Simon, Colin
- Josh: We need to tell everyone if you use Ice 3.4 server you have to use matching clients as well.
- Chris: maybe today or tomorrow myself and Josh can try it.
-
Josh: any other PR in other branches
- Andrew: specification folder changes
- Will: PR 25 more big ROI work.
- Josh: Since I am in the process of introducing those BIG changes, shall we go and do Hibernate 4.0 as well?
-
Next?
-
Hibernate 4.0
- Jason: how much work is that and how fare behind we are?
- Josh: we are on 3.5.6 and we will be jumping straight to 4.0.
-
Hibernate 4.0
- Done at 15:23 UK
-
Proposed for merge-blue
Glencoe Update
- Done at 15:30 UK
Minigroup Updates
- HIC
- Model
-
Web
- Ola: in process of reviewing/refactoring web tools
- Working on templates & static media files.
- Prepare foundation for common application base (cF. extensions)
- Will: screenshots of templates
-
FS:
- Colin: There is new branch based on earlier 909 proposal 2
-
Usability
- Scott: general discussion of tiding up google docs. More active use of alfresco, encouraging presentations, etc.
There were discussion with Jonathan Monk with providing more instances. * Jason: Jonathan is happy to host OMERO instances (pathology/Felts, EMDB, training) * Jason: Possibly for other institutes as well. Who pays the cost? * Josh: does this address monitoring issue. If this goes down they will come back to us, or we need to support it? * Jason: Not decided yet. For medium term, we need to provide some facilities to do it.
* High-level discussion how clients moving forward, integration and other businesses.Done at 15:38
Satellite Update
- ImageJ? Nothing new.
Copyright discussion spiralling into imglib2
Beta release has been pushed back, but now want to have it for the hackathon. Goal: Fiji2 on IJ2
-
"New" Satellites
- Others have contacted Jason. (cF. German Bioinformatics Network)
- Done 15:41 UK
-
"New" Satellites
Java 1.6 (in context of netCDF), see email to nitpick
- Curtis sent screenshots of soylatte. Main differences:
fonts are bad if from MacPorts (perhaps X-setting?) * Can’t resize Windows!
-
Jason: can we move to Java 1.6?
- Curtis: This research was just to see if we can recommend it to people as an alternative.
- Chris: doesn’t sound like we can. Curtis: certainly not recommended
- Will: only harming users … if bioformats it’s pervasive. Curtis: but possibly not a GUI issue.
- 10.5: there is a Java 6 for 64bit.
- Jason: is it enough time to email people in the mid-June we will switch?
- Chris: 10.4 hasn’t been updated for 4 years.
- Melissa: would be reasonable to bundle 1.6 SDK to Insight?
- Chris: less then 5% use 10.4
- Jason: Lets email that we will be moving and give potential solutions.
- Curtis: We could use retrotranslator which allows run compiled code against older Java version. Fiji requires 1.6 for development but use it produce a Java 1.5 jar.
- Melissa: biggest issue will be netcdf.
- Chris: would have to be very careful with 1.6 GUI widgets.
- Jason: first lets review statistics and then provide solution.
- Chris: we’ll also have Windows users
-
Jason: can we move to Java 1.6?
Encoding 2-d plane information in a URL (from Lee Kamentsky)
- Curtis: Grant mentioned OpenDAP. Any chance of using that?
- Will: what are the TODOs/actions?
- Jason: is it that they don’t want to use OMERO? Curtis: not necessarily
- Curtis: does this exist? Yes. Using imageId.
- Will/Ola: There are 2 urls. First image link in WebGateway viewer, second - render image region.
- Jason: Will, can you respond? OK.
Licensing for SCIFIO and OME-XML components (see email to nitpick) Started at 15:58 UK
- Latest version from offline discussion between Jason, Kevin & Curtis
- Jason: need to be careful with the form of the copyright (need to be incorporated)
- Curtis: e.g. at space science the individuals owned the copyright. Everyone listed.
- Jason: on some files, OME is listed, but it’s not incorporated. So added attribution.
- Jason: once legal, needs to be propagated to other parts of the project.
- Curtis: query into Wisconsin lawyer
- Chris: should be careful with polluting BSD template.
- Melissa: those changes are in ‘develop’, shall we merge it with ‘master’?
- Jason: 3 votes to move this to a branch?
- Curtis: need to have this for IJ2 beta.
- Finished 16:13 UK
Any other business (<5 mins)
-
PRs & screenshots/movies
- Josh: J-M wanted me to mention. Once PR has various tickets from different stories.
-
Chris: discussed in the web meeting.
- one bug/rfe per component (insight/web/server)
- same strategy of ticket per bug
- Finished 16:17 UK (kicked out)
-
Advertising Docs
- Our own?
- Monash docs ?
- Use of OMERO by CLS-- a usability project?
-
PRs & screenshots/movies
Action
* Jean-Marie: look into QAs
* Josh: answer https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=919
* Will: ask for the script submission
* Chris/Will: define SVS plan
* Josh: forward Columbus issues.
* Colin: create tickets from movie talk (“Summary to be turned into tickets”)
* Josh: merge-blue with Ice & Insight builds. Hand-off to Chris and homebrewers.
* Josh: start defining short-/med- term monitoring of servers
* Josh: get 64bit 10.5 stats. (Windows users?)
* Will: respond to Grant’s email about the web urls for getting data
* Curtis: resolve WISC copyright rules
* Josh: Add PR/screenshot discussion to next week’s agenda