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You are here: Home Community Minutes Conference Calls 2010 2010-09-23 Thursday Meeting

2010-09-23 Thursday Meeting

Attending: Brian, Andrew, Colin, Josh, Jason, Melissa, Will, Ola, Brian Jones


Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

  1. Accepting minutes from last meeting

  2. Matters Arising (<10 mins)

    • Need a bug triage for 4.2.1
    • Discuss IContainer to delete queue delete items (from Tuesday)
    • Andrew: send out SPIM results, possibly scan the drawn notes (pending)
    • Andrew: look over your modelling story, pick top item for us to complete before ASCB link
      • My preferred task (1st, 2nd, 3rd choice, not an order to do them)
      • 1 N-Dim
      • 2 Detectors
      • 3 Transform Matrix (Needed for big images, derived images, tiled images)
  3. Sprint Status

    • We have one more week for this iteration. The sprint will now end 30th September 2010
    • Status Update
      • Delete issues (20 mins)
        • Added phase II requirement in "Unscheduled":
        • Allocated time on Tickets
        • Ticket Review
      • VMs (10 mins)
        • Ticket Review (all tix need time entered)
      • Table bugs (??)
      • Windows jobs on Hudson
      • CellCog: disable or polish?
      • EMDB: close story or push?
  4. Meeting presentations on Alfresco (2 mins)

  5. What does it mean to be 'Available' on Jabber? (2 mins)

  6. Branch, package and internal testing (i.e., nightshade) for 1st week of October?

  7. Email and Forum Review - checked at (5 mins)

    • Email -

      • [ome-devel] omero beta 4.2.0: omero.web does not load all plate thumbnails and reports exceptions
      • [ome-devel] RuntimeException with ScanR importer.
    • Forums -

      • Re: Centos 5.3 link
      • Re: Also cannot login to webadmin link
      • Re: Moving binary repository link
      • Further information link
      • Omero Web mod_python on osx 10.6 link
      • Omero Web production server failure link
      • init.d startup questions link
    • QA - link

      ID  Status  User/email  Type    Created Selected file   Comment Error
      2774    new markov@sysbi... Insight 4.2.0   2010 09 23  -   -   java.lang.Exception: org....
      2773    new icaoberg@cmu... Insight 4.2.0   2010 09 22  -   -   java.lang.Exception: org....
      2772    new cjw@stowers.... Insight 4.2.0   2010 09 22  -   I right clicked and selected s...   java.lang.Exception: org....
      2771    new unknown Insight 4.2.0   2010 09 22  -   -   java.lang.Exception: org....
      2770    new ajdmelvin@du... Importer 4.2.0-DEV  2010 09 22  6_1h_01_R3D_D3D.dv  It's still doing it chris. ra...    java.lang.ArrayIndexOutOf...
      2748 - 2770 new ajdmelvin@du... Importer 4.2.0-DEV  2010 09 22  1_0h_01_R3D_D3D.dv  It's still doing it chris. ra...    java.lang.ArrayIndexOutOf...
      2747    new k.j.walker@d... Insight 4.2.0   2010 09 22  -   opening a second image window....   java.lang.Exception: org....
      2746    new jay_copeland... Importer 4.2.1-DEV  2010 09 21  plate1.HTD  This is the first attempt at u...   Ice.ObjectNotExistExcepti...
      2745    new markov@ioc.e... Importer 4.2.0-r757 2010 09 21  image2.ome.tif  -   java.lang.NullPointerExce...
      2710    new Importer 4.1.1-r592 2010 09 13  Cell01_1.ome.tif    -   java.lang.RuntimeExceptio...
      2709    new jay_copeland... Importer 4.2.1-DEV  2010 09 13  HCC1187_A01.pnl This is my first attempt at im...   loci.formats.FormatExcept...
      2699    new anlkae@uks.e... Insight 4.2.0   2010 09 11  -   tried data retrieval    java.lang.Exception: org....
      2691    new unknown Importer 4.2.0-DEV  2010 09 07  A8_fish2_headareazoom3.lsm  Data import error   java.lang.IllegalArgument...
      2690    new unknown Importer 4.2.0-DEV  2010 09 07  A8_fish2_headareazoom2.lsm  Data import error   java.lang.ArrayIndexOutOf...
      2685    new team-sysadmi... Insight 4.2.0   2010 09 02  -   I was opening a dataset consis...   java.lang.Exception: org....
  8. Any Other Business (<5 mins)

    • New Printer - Standard LifeSci Colour Printer - HP Colour LaserJet 3525dn - £467.52/EA
    • ASCB - Jason/Andrew talk to get attendee list add names to hotel rooms before end of month.

In Attendance: Brian, Andrew, Colin, Jason Ola, Josh, Will, Melissa, Brian Jones


  1. Matters Arriving

    • Bug Triage: Going through this tomorrow morning when everyone is back
    • IContainer, etc: Josh isn't sure this will get done in time. Discuss tomorrow with Jean-Marie
    • SPIM Results: Being carried forward
    • Andrews preferences before ASCB listed above
      • Josh: Transform Matrix seems like a priority
      • Jason: And N-Dim as well. Model needs to be shown
      • Josh to Jason: Is there a deadline you're looking for with N-Dim?
        • Jason: Not sure, need to know how hard this will be. Several interested parties want this.
  2. Sprint/Delete:

    • Josh: Went over #2615 and removed unneeded (for this release) to #2911
    • Colin: Seeing thumbnails/pixels disappearing now, but this is partially working
      • Josh: Probably needs a test
    • Will: delete looked fine (several images at once didn't work initially)
      • issue about collaborative deletes - my tags get deleted. Should it be this way?
      • comments on multiple images deleted if one of the images its attached to is deleted (this is a bug)
        • Will: its been added to one of the tickets (#2767)
        • Josh: This could take a few days to fix
    • Josh: major issue is #2792.
      • Blockers could take a week. We should draw a line (after this one fix?)
    • Josh: Branching by next Thursday might not be doable
      • Jason: Branch in two weeks (first week of October [4-6th])
    • Tickets without Timing
      • Lots of tickets without timing on them (in delete/#2767)
        • Job for tomorrow's traige (tomorrow morning)
      • Ola: Objects are being put to Queue in Web now.
        • Also has 'working' bar with queue information
      • Josh: Ola, do you need folks to test?
        • Ola: Pretty simple, Colin/Jason can test when its ready
  3. Sprint/Other:

    • VMs
      • Need Chris to setup a box with virutalization; 10.*.14[89] don't
      • Scripts working.
      • People at conferences excited about it
      • May need to add sample data
      • Enter times on the tickets
    • Table
      • There are some bugs here. Josh fixed a few. One major one here.
        • Needs to be group permissions aware.
        • HDFs downloading as ND files - needs fixing.
        • Where do we draw the line here?
        • Jason: 4.2.1 is 'set' really. If we can squeeze them in great, but lets not push
    • Windows (on Hudson)
      • All our Windows tests are failing (for a few months?). This needs fixing.
        • Jason: Why?
        • Josh: May be some persmissions problems from some other user. May need a controlled environment
        • Could be an easy fix (hopefully)
    • CellCog
      • Currently only Mac-only. Need to make this clear or make it work elsewhere
      • Jason: Doesn't need to be in 4.2.1.
      • Will: agreed
    • EMDB
      • Will has pushed most of his tickets forward.
      • Has fixed main login problem (last week). EMDB pretty stable now.
      • Should be safe to send link.
      • Scripting service/analysis is NOT working though.
      • Scripting service framework won't return feedback if it crashes (so not fit)
      • Everything else in the movie Will did should be working
      • Needs some stress testing
      • Jason will test. (data under #1080)
      • Should Will contact people from Oxford meeting about testing it?
        • Will is away next week (but should be online regularly)
        • Jason will give Will feedback on the weekend and then send emails out to prospective testers after that
  4. Other

    • All presentations should be on Alfresco, and everyone should have access
      • ALL: Limit the emailing of these things! (they are big)
      • Andrew: in 2 different sites (Swedlow lab & OME Stuff). Where should I put things?
        • Jason: Lets use OME Stuff
        • Andrew: will move it over.
      • What does the 'public' folder mean?
        • Jason: That's just stuff for posters, etc. Should not matter if we go to OME Stuff
    • Jabber: Don't leave yourself in Jabber if you're not around - gets confusing!
      • Should be ok if you make sure you use your idle away status correctly!
  5. Emails / forums / QA

    • Web
      • (ome-devel) Bram needs a response. Ola will do it.
      • Will also respond to the other few that she hasn't emailed yet.
      • Josh will talk to Bram
    • QA/Insight
      • Note for Jean-Marie to handle his QA
    • QA/Import
      • Melissa's ArrayIndexOutOfBounds wasn't related to QA
      • Brian: patch last week for AIOOB for DV files
      • Need to retest (Chris updated nightshade)
      • Brian will check if the tickets are fixed.
  6. Any other business

    • Printer will be ordered
      • Andrew and Jason will sort it out (see action items)
    • ASCB:
      • Andrew needs to have a meeting with Angie to work out details
  7. Meeting summaries

    • People liked poster
    • Had people 'handing in code for integration', but not doing the integration themselves
    • Some examples of people without infrastructure to setup of OMERO
      • Jason: Had similar examples elsewhere - common problem
    • Colin: Might it be worth dedicating a Tuesday to short 'catchup' presentations?
      • Perhaps in two Tuesdays from now (Oct. 5th)?
    • MIFOBIO 2010 - This is 'the' meeting in France for light microscopy
      • Lots of Vendors
      • Gave Demo with latest server code (12 stations or so)
      • Lots of positive feedback (and want everything of course)
      • Lots of people using/evaluating it already
      • B.Jones: Any surprises?
        • Jason: How big it was is a surprise

Action Items

  • Colin: Email folks about tomorrows triage meeting (in the morning)
  • All: friday morning bug triage and delete triage (with ticket times) - incl. IContainer discussion
  • Colin: Please add a test for thumbnail/pixels issue
  • Will/Josh: comments with muiltiple links being deleted. Needs ticket
  • Ola: Get a setup for Jason to test new web delete queue by mid-next week (Mage perhaps?)
  • Jason: Send email to nitpick with 'publically safe' images we can use for sample data
  • Chris: Can we get a new (controlled evironment box) for Windows tests?
  • Jason: Please test the EMDB stuff again
  • After Jason tests, Will/Josh move all tickets out of 4.2.1
  • Andrew: Go though Alfresco and move OME stuff to OME stuff.
  • Chris: What's up with forum messages being 'bumped' now? Did we loose some new stuff?! (Josh after refresh looks ok. weird)
  • Jean-Marie: QA items
  • Brian: Double check import QA issues
  • Andrew: Email Jason with account numbers so printer can be picked.
  • Andrew: Meet with Angie about ASCB details
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