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You are here: Home Community Minutes Conference Calls 2012 2012-04-03 Tuesday Meeting

2012-04-03 Tuesday Meeting

Attending: Andrew, Jean-Marie, Sebastian, Elwood (notes), Emma, Chris, Colin, Roger, Ola (excused 16:15), Will, Jason, Carlos, Liza, Gus, Scott, Stick

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

  1. Matters Arising (<10 mins)

    • Actions
      • Liza/Josh: update the ohloh logos:,
      • Everyone: again, please look for duplicates on ohloh:, (Especially: Brian, Donald, Chris, Carlos)
      • Andrew: improve handling of website feedback - done - now mails website-feedback list (andrew and emma)
      • Ola: add webstart, downgrade, webadmin, basket to web discussion (see stories on milestone page)
  2. Email and Forum Review - checked at (5 mins)

    • Email -

      • Haari Jäälinoja - Re: [ome-users] Issues with NewUserGroupBean implementation (thread with Josh - last mail from Haari on 30 Mar - does it need a reply?)
    • Forums -

    • QA -

          -- -- Add list indented 12 spaces
          ID  Status  User/email  Type    Created Selected file   Comment Error
          4266    new ian.dobbie@b... Insight 4.3.3   2012 04 02  MukB_D_A_ypet_07.dv Hi We are having problems uplo...   java.lang.IllegalArgument...
          4265    new fhauser@ucsd... Web 4.3.4-dbcb  2012 04 01  -   still trying to fix Traceback (most recent ca...
          4264    new Importer 4.3.3-00d1 2012 03 30  ...age Display-Acquire CCD -0.tif   Images were exported from FEI'... 1: b...

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

  2. Sprint Bug Report (5 mins)

    • New bugs: 12 (6 critical, 1 major, 5 minor)
    • Total bugs: 97 (4 blocker, 12 critical, 29 major, 52 minor)
  3. Colin: FS presentation (45 mins)

  4. 4.4 Decisions (15 mins)

  5. Testing (10 mins)

  6. Satellite Update

  7. Glencoe Update

  8. Any other business (<5 mins)


Attending: Andrew, Jean-Marie, Sebastian, Elwood (notes), Emma, Chris, Colin, Roger, Ola (excused 16:15), Will, Jason, Carlos, Liza, Gus, Scott, Stick

Pre-Meeting All addressed, repsonded and covered

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • None
  2. Sprint Bug Report (5 mins)

  3. New bugs: 12 (6 critical, 1 major, 5 minor)

  4. Total bugs: 97 (4 blocker, 12 critical, 29 major, 52 minor)

    • Emma: Total 97, close to 100
    • Jean-Marie: testing branches effort, will go down after testing the web, 10 new ones from Gus and Scott in Insight, as soon as those branches go in they will go down
      • Talked to Will & Josh that josh had chmod branch and we merged it in to develop. Tests written on it, so Will Carlos and I can start work. So in place for when Josh comes back
    • Ola: Email for an import issue using FS
      • Chris: Size of file an issue?
      • JM: using FS
      • Ola: no imports found
      • Chris: up logigng to debug
      • Ola: tried set of images and a single image
      • Colin: logging on cls-dev machine
      • Chris: trtack exception, probelm with those files is to short circuit the min-max calculation
        • Trying to calc min max on a large jpeg, decompressing
        • Colin: If not a big image is done inline
  5. Colin: FS presentation (45 mins) - Start 14:33

    • fs-lite and import
    • first few slide repeated from July, old import process and looking at new one
    • all in ticket 909
    • numbered files are not useful / helpful are database related
    • import libraries on the client
    • big images added a bout a year ago
      • we always archive the big image
      • after import a separate process worked through the pyramid generation on big images
    • lots of duplication/ triplication of data
    • templated directory structures
    • on import tries to work out a unique path
    • new import process gets the unique path and then uploaded to the server
    • control handed over to the server processing of uploaded file
    • dropbox was duplication but under new scheme it doesnt
    • down side is we have to access the pixel data from the original file, some overhead to work out for different file formats
    • no performance testing yet, in progress
    • file path clashing issues, common file names, e.g. log files, summary files
    • orignal metadata needs to be generated on import
    • notifications
    • cancellation after all files have been uploaded
    • discussion over exposing file system
    • Roger: read-only after import?
      • Chris/Colin: no they are writable would be an admin concern
    • Jason: file system level i deleted everything in 2012, in pricipal it is recreatable if i have original data.
      • Chris: only problem is we dont summaries import effectively in the database. Wouldnt be able to tell which file created which image.
        • LEI stores summary file, to recreate the information it would require a lot of work
    • Jason: Archiving?
      • Chris: get it for free

    Done 15:30

  6. 4.4 Decisions (15 mins)

  7. Jason: 4.4 release of fs?

    • Chris: do or dont, no inbetween
    • Colin: perf. testing this week
    • Jason: CRUK data?
    • Colin: cls image repository testing
    • Chris: HCS use case testing
    • Emma: wont make 4.4 but some time after.
    • Chris: keep Colins branch going but release to a subset of installations
    • Chris: impacts ALL users
    • Colin: preview versions?
      • Marking importer as deprecated, importer less deprecated than stuff that doesnt work
    • Chris: do we release this to the wild? or do we approach the proper use case, showing them the file system by default?
    • Jason: trials at 10 or so places
    • Chris: all imports are on the server
  8. Emma: meeting on Friday

    • Jean-Marie: some decisions pending, channel/logical channel, rendering (4.4.1)
    • Jean-Marie: FLIM floating point -> int values?
      • Jason: yes
    • Jean-Marie: large pixel ranges, image comes in but still black
      • Chris: we dont support any more than 16bit of dynamic range
      • J-M: min max range is bigger
    • Jean-marie: Insight headless, made good progress, from Dresden. For multi-thread need to do some cleaning. hopefully in 4.4 maybe, 4.4.1 definitely
    • Chris: Rendering Engine ones not in 4.4
    • Chris: Channel/Logical Channel we need to decide collectively, impacts everyone!
      • Jean-marie: The other model changes, naming conventions have been made.
      • Will: Channel/Logical channel merge is less imapct?
      • Chris: equivalent impact, properties move, layer of heirarchy moves, queries updated, objects removed from mapping level, not trivial
      • Jean-Marie: omero matlab, omero py, folloing ian's email to allow for them to look at it. For name change, get channel -> get logical channel
      • Chris: only place in entire model where we have inconsistency if we don't do it in structure
      • Will: saving breaking change for after 4.4
      • Jason: amount of time to accomodate that, additional time to do logical channel? sprint or 7?
      • Jason: project wide sprint,
      • Chris: all docs, clients, servers, insight, insight gateway
      • Will: no exposure in blitz gateway, there is documentation though
      • Chris: wrapper objects written by hand, all needs to be updated, scripts
      • Jason: extended by 2 weeks? The model is correct!
      • Will: seeing as were doing it as a breaking change release.
      • Chris: whole bunch of havoc by removing many-one, in omero you can have multiple pixels, not prevented.
      • Jean-Marie: extend by another sprint.
      • Elwood: Testing after the work has been done.
      • Emma: Decision made, do it and extend by 2 weeks.
    • Jason: Code generation / database?
      • Chris: Code-gen done
      • Chris: Database changes pending
      • Andrew: Changes are detailed on tickets 8084,5,6
      • Jason: OME calendar, schedule between now and Paris
      • Final model changes
  9. Testing (10 mins) - 15:50

    • Emma: testing being generated. Need thought and discussion on who and what will be allocated. Come next Tuesday / after, expectations are understood.
    • Emma: Next Tuesday people are away so schedule for later this week.
    • Jason: Get some prep done before we meet
      • Making it available and what should be tested
    • Chris: localised changes we've been doing okay. ON database changes it effectively test everything, several weeks form that, at least 2 weeks from that if not 4-5 from being able to start that.
    • Jason: between now and then is there the possibilty to test what is in place now?
    • Chris: coverage on file formats is good from Roger
    • Chris: whole scale testing apart from small stuff is Doms UI in web client. Nearest wholescale testing operation.
    • Jason: need to address issue with Scott and Gus how soon do we hand off areas, next full on testing is web UI
    • Chris: as soon as the UI is functionally complete, need to touch whole interface elements.
    • Will: plugin branch has some wide spanning changes too
    • Jason: articulate what is needed in terms of testing the UI.
    • Chris: Probably not everyone on the entire team.
    • Ola: across all web browsers, the new UI
    • Gus: if testing is massive, is it doable in the timescale?
    • Gus: big backlog for user support team already. I browse and fiddle to find problems.
    • Jason:
        1. need a schedule for when the web UI is going to be available, within a week.
        1. Then we need a schedule for when model will be changed and who will be available.
      • 3.1 If UI testing how can people get access
      • 3.2 What the process will be when we start testing?
        • Testing scenarios has been a bit too atomic before.
      • Chris: localised testing has been more thorough.
      • Jason: waste of time to repeat those, what is the right way to test the application before release?
    • Jean-Marie: what was quite efficient was when we did movies with a real workflow.
    • Chris: you will come across workflow related issues, where we accept that its the way it works
      • Advantage is we're doing it soon enough to potentially resolve some of those
    • Jean-Marie: Use movie list as start of test plan.
      • Scott: we need enough details for someone to follow.
    • Gus: needs context when testing to better find and follow expected workflow.
  10. Satellite Update - 16:15

    • Mailing list checklist
    • Oxford short list candidates
  11. Glencoe Update - 16:17

    • Big images - scale and quantity
    • Server requirements for performance needs documenting
  12. Any other business (<5 mins)

  13. Chris: hudson problems with builds, working more with it. Speaking to stick for next web testing

Actions * Jean-Marie: Talk to melissa about a QA issues (4264, 4266) * Chris: Talk to stick about web testing infrastructure.

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